title: 4_siVPS4AB#2

city: Warszawa

first: Krzysztof

last: Goryca

address: Banacha 2c

department: CeNT

country: Poland

institute: Uniwersytet Warszawski

data_processing:
torrent mapper, version 5.0.4
htseq-count, version 0.6.0, default parameters
DESeq2, version 1.18.1, normalization
removal of features with less then 10 counts based on the sum of normalized counts across all samples, removal of non-protein coding features
Genome_build: hg19
Supplementary_files_format_and_content: DESeq2 normalized count matrix

growth_protocol: Human colorectal carcinoma cell line HCT116 was obtained fom Horizon Discovery Ltd (cat# HD PAR-073). Cells were grown in RPMI medium (Sigma-Aldrich, R0883) supplemented with 10% (v/v) fetal bovine serum (FBS, Sigma-Aldrich, F7524) and 2 mM L-glutamine (Sigma-Aldrich, G7513). Cells were splited 1:10 twice a week. During the study, cells were regularly tested for mycoplasma and the identity of  HCT116 cell line was confirmed by short tandem repeat (STR) profiling performed by the ATCC Cell Authentication Service.

extract_protocol:
Total RNA was isolated with RNeasy Mini Kit (Qiagen, 74104) followed by on-column DNase  digestion according to manufacturer’s protocol.
Library was prepared with the Ion AmpliSeq Transcriptome Human Gene Expression Panel (Thermo Fisher, USA)

treatment_protocol: 1.15x105 of HCT116 were seeded per well of 6-well plate. Next day, cells were transfected with siRNA using Lipofectamine RNAiMAX transfection reagent (ThermoFisher Scientific, 13778150) and protocols provided by the manufacturer. In controls cells were transfected with 60 nM of non-targeting siRNA (siCTRL#1), for single VPS4A or VPS4B depletion a combination of 30 nM of siCTRL#1 and 30 nM of on-target siRNA (siVPs4A or siVPs4B) was used,  and for simultaneous knockdown of two VPS4 (A+B) 30 nM of each siRNA duplexes was used. The following Pre-Design or Validated Ambion Silencer Select siRNAs (ThermoFisher Scientific) were used: non-targeting siCTRL#1 (4390843); on-target siVPS4A#1 (s25966), siVPS4A#2 (s25968), siVPS4B#1 (s18272), siVPS4B#2 (s18273). Cells were collected 72 h after transfection.

tag: sirna

tag: batch

value: d


title: CordBlood3-RNA

status: Public on Nov 16 2019

type: SRA

city: New York

first: Caleb

last: Lareau

state: New York

address: 417 E 68th St, Zuckerman - ZRC 1132

country: USA

institute: Memorial Sloan Kettering

library_source: transcriptomic

data_processing:
Adapter sequences were trimmed from FASTQs using cutadapt.
Reads were aligned to the hg19 reference transcriptome using STAR two-pass mode
Gene abudances were quantified using STAR geneCounts
Genome_build: hg19
Supplementary_files_format_and_content: Raw gene abdunace counts per-library as described in the data processing steps

molecule: total RNA

organism: Homo sapiens

source_name: newborn erythroid cells

extract_protocol:
Cells were incubated with 100 μg/ml of cycloheximide (Sigma Aldrich) for 5 minutes at 37°C, washed twice with ice-cold PBS containing 100 μg/ml of cycloheximide and lysed in 10 mM Tris-HCl (pH 7.4), 5 mM MgCl2, 100 mM KCl, 1% Triton X-100, 3 mM DTT, 100 μg/ml cycloheximide, 500 U/ml RNasin (Promega) and 1x Complete Protease Inhibitor, EDTA-free (Roche). Lysates for ribosome profiling were prepared and ribosome protected RNA fragments (RPFs) were isolated as described previouslywith the following modifications: rRNA was depleted using the RiboMinus Eukaryote Kit v2 (Thermo Fisher Scientific) by following the manufacturer’s instructions. rRNA depleted RPFs were purified with the Zymo RNA Clean & Concentrator-5 kit by following the manufacturer’s instructions for small RNAs. PAGE purification of RPFs was performed as described previously and resulting RPFs were dephosphorylated in FastAP mix (19.5 µl H2O, 2.5 µl 10x FastAP buffer (Thermo Fisher Scientific), 2.5 U FastAP enzyme (1 U/µl; Thermo Fisher Scientific), 0.5 µl Murine RNase Inhibitor (New England Biolabs)) and incubating for 20 minutes at 37°C. In the meantime, polynucleotide kinase mix was prepared (57 µl H2O, 10 µl 10x PNK buffer (New England Biolabs), 0.5 µl Murine RNase Inhibitor, 6.5 µl T4 PNK (10 U/µl; New England Biolabs), 1 µl TURBO DNase) and added 75 µl to each 25 µl sample and incubated 20 minutes at 37°C. RPFs were purified with the Zymo RNA Clean & Concentrator-5 kit following the manufacturer’s instructions for small RNAs.
RNA was eluted in 7 µl H2O, 1.5 µl DMSO and 10 pM 3’ adapter (/Phos/AGATCGGAAGAGCACACGTCTG/ddC) were added before denaturation at 65°C for 2 minutes and transferring samples to ice. Subsequently, 11 µl ligation mix was added (2 µl 10x T4 RNA ligation buffer (New England Biolabs), 0.3 µl DMSO, 0.2 µl ATP, 0.3 µl RNAse inhibitor, 7 µl 50% PEG 8000, 1.2 µl T4 RNA Ligase 1 High Concentration (New England Biolabs)) using low retention pipette tips and incubated 1 hour at 23°C with agitation. Ligation reactions were purified to remove free 3’ adapter using Silane bead purifications. For each reaction, 15 µl Silane beads (Thermo Fisher Scientific) were washed twice in 1 ml RLT buffer (Qiagen), beads were resuspended in 60 µl RLT, and 60 µl beads in RLT was combined with 20 µl ligation reaction. 0.7 volumes 100% ethanol were added and incubated for 10 minutes at room temperature. Supernatant was removed and beads were washed twice with 70 % ethanol before eluting air-dried beads in 10 µl H2O. Next, 10 pM reverse transcription primer (/5’biotin/GACGTGTGCTCTTCCGA) was added and samples were denatured at 72°C for 3 minutes before transferring to ice. To each reaction 7 µl reverse transcription mix (0.25 µl H2O, 2 µl 5x Smartscribe first strand buffer (Takara), 0.25 µl RNase inhibitor, 2 µl Smartscribe RT (Takara), 2 µl dNTP, 0.5 µl 20 mM DTT) were added and samples were incubated at 42°C for 15 minutes. Next, 2 µl template-switching oligo (5'biotin/TACACGACGCTCTTCCGATCTrGrG+G) were added and samples were incubated 90 minutes at 42°C, followed by 10 minutes at 70°C. Samples were purified with Silane beads and subjected to PCR amplification using 2x NEBNext Q5 Hot Start HiFi PCR Master Mix (New England Biolabs) as described previously. Amplicons migrating at a size of ~157 bp were subjected to two consecutive rounds of gel purification. For preparation of mRNA sequencing libraries, total RNA was extracted with the Direct-zol RNA MiniPrep Plus Kit (Zymo Research) according to the manufacturer’s instructions. Total RNA was poly-A selected using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs) according to the manufacturer’s instructions. mRNA was eluted in 27 µl H2O, 3 µl 10x FastAP buffer were added and RNA was heat fragmented for 3 minutes at 91°C. Fragmented RNA was end-repaired, adapter ligated, reverse transcribed and PCR amplified.

treatment_protocol: CD34+ HSPCs from adult and newborn were differentiated until day 7 (proerythroblast stage) for examining ribosome profiles.

tag: cell type

value: hematopoetic cells

value: newborn erythroid cells


title: 4_siVPS4AB#1

tag: cell line


title: 4_siVPS4B#1


title: 4_siVPS4B#2


title: Adult2-ribosomeprofiling

data_processing:
Library strategy: Ribo-seq
Adapter sequences were trimmed from FASTQs using cutadapt.
Reads were aligned to the hg19 reference transcriptome using STAR two-pass mode
Gene abudances were quantified using STAR geneCounts
Genome_build: hg19
Supplementary_files_format_and_content: Raw gene abdunace counts per-library as described in the data processing steps

source_name: adult erythroid cells

value: adult erythroid cells


title: CordBlood3-ribosomeprofiling


title: LIN28B-Rep2-input (CLIP-seq)

data_processing:
Adapter sequences were trimmed from FASTQs using cutadapt.
Reads were aligned to the hg19 reference transcriptome using STAR two-pass mode
Peaks were called using MACS2 with parameters --nomodel --nolambda --bw 100 --extsize 50
Downstream processing was performed using the GenomicRanges and IDR to call consensus peaks
Genome_build: hg19
Supplementary_files_format_and_content: Peaks called for both replicates using data processing steps above

extract_protocol:
NA
Cells were crosslinked using 0.4 J/cm2 of 254 nm UV light, pelleted by centrifugation and washed twice with ice-cold PBS. Cell lysates were prepared as described in Hafner et al. 2010 Cell 141, 129–141. RNA was partially digested using RNase I, followed by addition of RNase inhibitor and DNA digestion. Insoluble material was removed by centrifugation and lysate was pre-cleared by incubating with Protein A/G magnetic beads. We added the pre-cleared lysates to antibody-coupled beads and incubated overnight at 4 °C. The following day, we washed the beads 4 times in IP wash buffer (50 mM HEPES pH 7.5, 150 mM KCl, 0.5% (v/v) NP40, 0.25 mM DTT, complete EDTA-free protease inhibitor cocktail). Protein-RNA complexes were resolved by SDS-PAGE, followed by transfer to a nitrocellulose membrane. RNA was isolated by proteinase K treatment and phenol-chloroform extraction. We constructed RNA sequencing libraries using the SMARTer smRNA-Seq Kit (Clontech) by following the manufacturer’s instructions.

tag: developmental stage

value: newborn

tag: antibody

tag: rna composition

value: Total RNA


title: 4_siVPS4A#2


title: Adult2-RNA


title: LIN28B-Rep1-input (CLIP-seq)

value: rRNA-depleted


title: LIN28B-Rep2 (CLIP-seq)


title: 5_siVPS4A#1

value: e


title: LIN28B-Rep1 (CLIP-seq)


title: 4_siVPS4A#1


title: 5_siCTRL#1


title: 4_siCTRL#1


title: Adult1-ribosomeprofiling


title: 3_siVPS4AB#1

value: c


title: 3_siVPS4AB#2


title: 3_siVPS4B#2


title: Adult3-ribosomeprofiling


title: 3_siCTRL#1


title: 3_siCTRL#2


title: 3_siVPS4A#2


title: 3_siVPS4B#1


title: 4_siCTRL#2


title: 3_NT


title: 2_siVPS4AB#2

value: b


title: 4_NT


title: 3_siVPS4A#1


title: 2_siVPS4AB#1


title: KO1_24h

type: RNA

city: Paris

first: Sebastian

last: Amigorena

address: 26 rue D'ulm

country: France

institute: Institut Curie

hyb_protocol: Labelled DNA was hybrized on the Affymetrix Mouse Gene 2.1 ST processed on an Affymetrix GeneTitan device.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Microarray data were carried out with R (version 3.1.0) using packages from the Bioconductor. Raw data CEL files were used and the quality control analysis was performed using ArrayQualityMetrics package. The raw data were preprocessed using the RMA (Robust Multi-array Average) method available in oligo package. Gene expression levels were analyzed on a base-2 logarithmic scale.

label: biotin

organism: Mus musculus

label_protocol: For each condition, RNA was employed to synthetize cDNA according to the standard Affymetrix protocol.Affymetrix GeneTitan device.

growth_protocol: Naïve CD4 T cells from littermate WT and TRIM28KO mice were enriched by magnetic selection and sorted by flow cytometry.

extract_protocol: RNA was extracted using Rneasy Micro Kit (QIAGEN) according to the manufacturer protocol. A column DNAse treatment was included (QIAGEN).

treatment_protocol: Cells were stimulated for indicated times with anti-CD3 (plate-bound) and anti-CD28 (soluble)

tag: genotype

tag: tissue

value: CD4 T cells


title: WT1_72h

source_name: wild-type

value: wild-type


title: KO3_72h


title: WT3_24h


title: KO2_24h


title: 2_siVPS4B#2


title: KO1_72h


title: WT2_72h


title: WT1_24h


title: 2_siVPS4B#1


title: KO2_4h


title: KO3_24h


title: WT3_72h


title: WT2_24h


title: 2_siCTRL#2


title: WT3_4h


title: 2_siVPS4A#2


title: 2_NT


title: KO3_4h


title: 2_siVPS4A#1


title: KO2_72h


title: KO1_4h


title: 1_siVPS4AB#2

value: a


title: WT2_4h


title: 1_siVPS4B#2


title: 1_siVPS4AB#1


title: 1_siVPS4A#2


title: 1_siVPS4B#1


title: 1_siCTRL#2


title: 2_siCTRL#1


title: MitoT+ sample 4

city: Santiago

first: Vinicius

last: Maracaja-Coutinho

state: Santiago

address: Santos Dumont 964

country: Chile

institute: Universidad de Chile

data_processing:
Trimming was performed using Trimmomatic version 0.36
Mapping was performed using HISAT2 version 2.0.5
SAM files generated on the mapping process were used as input to the Cufflinks protocol
GTF annotation file for Cufflinks protocol was recovered from Ensembl database for the human genome GRCh38
Genome_build: GRCh38

source_name: Peripheral blood

extract_protocol:
Peripheral blood mononuclear cells were isolated and MitoCepted previosly FACS sorting of CD3+ MitoT+ and CD3+ MitoT- cells. Total RNA was extracted from 500,000 FACS-sorted cells using RNeasy Micro Kit from Qiagen (Cat# 74004)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: CD3+ cells

value: Peripheral blood

tag: group

value: mitocepted (MitoT+)


title: in_vitro-matured_SCbeta_ATAC_72h

city: Cambridge

first: Juan

middle: R

last: Alvarez-Dominguez

state: MA

address: 7 Divinity Ave

department: Stem Cell and Regenerative Biology

institute: Harvard University

library_source: genomic

data_processing:
Sequencing reads were mapped to the human hg19 reference genome assembly using bowtie2 (Langmead and Salzberg, 2012) with default parameters. Peak calling was performed using MACS2 (Zhang et al., 2008) with default parameters, “--nomodel --shift 37 --extsize 73” to bypass building a ChIP-based shifting model and instead shift read 5’-ends and extend in the 5'->3' direction by a half-nucleosome size (73bp), and  “--broad --qvalue 0.01” to composite broad regions of read enrichment with a minimum FDR q-value cutoff of 0.01.
Genome_build: hg19
Supplementary_files_format_and_content: Tab delimited file with peak coordinates

molecule: genomic DNA

source_name: HUES 8 hESC line

growth_protocol: Undifferentiated stem cells were maintained as aggregates in supplemented mTeSR1 medium (StemCell Technologies) using spinner flasks (Corning) set at a 70rpm rotation rate in a 37ºC 5% CO2 incubator. Directed hPSC differentiation into islet cells was conducted as described in the methods of (Alvarez-Dominguez et al. 2019).

extract_protocol:
Live cells (typically ~50,000) were pelleted and tagmentation was performed at 37ºC for 30min as described in (Buenrostro et al., 2013). Briefly, cell pellets were resuspended in buffer containing Tn5 Transposase (Nextera DNA Sample Preparation kit; Illumina), incubated at 37ºC for 30min, and DNA was isolated using the MinElute PCR purification kit (Qiagen).
Tagmented DNA was PCR-amplified for 10 cycles and purified using AMPure XP magnetic beads (Beckman Coulter). Double-sided AMPure cleanup to remove high-molecular-weight fragments was conducted by incubation of double-concentrated AMPure beads added at 0.55x volume to the PCR reactions, followed by cleanup with a 1x AMPure volume. Sequencing libraries were pooled and sequenced on a HiSeq 2500 instrument.

value: HUES 8 hESC line

value: hPSC-derived beta cell

tag: Stage

value: entrained to circadian metabolic rhythms


title: MitoT+ sample 3


title: KO1_0h


title: WT1_4h


title: WT2_0h


title: Th1_KO_REP3

extract_protocol: RNA was extracted using Rneasy Micro Kit (QUIGEN) according to the manufacturer protocol. A column DNAse treatment was included (QUIGEN).

treatment_protocol: Cells were stimulated for indicated times with anti-CD3 (plate-bound) and anti-CD28 (soluble), in Th0, Th1, Th2, Th17 or Treg conditions.


title: 1_siVPS4A#1


title: Naive_WT_REP1


title: WT3_0h


title: KO2_0h


title: Naive_KO_REP2


title: MitoT- sample 4

value: MitoT-


title: WT1_0h


title: Th17_KO_REP3


title: Treg_KO_REP3


title: Th0_KO_REP3


title: Naive_KO_REP3


title: Treg_WT_REP3


title: 1_NT


title: MitoT- sample 1


title: 1_siCTRL#1


title: Th17_WT_REP3


title: Th2_WT_REP3


title: MitoT+ sample 1


title: MitoT+ sample 2


title: Th0_WT_REP3


title: KMS11_shPRDM5_1i

city: Pamplona

first: Xabier

last: Agirre

state: Navarra

address: Pio XII, 55

department: Oncology

country: Spain

institute: CIMA

description: KMS11 cell line infected with the shRNA#1 targeting PRDM5 prior to shRNA expression induction

data_processing:
Illumina Casava software used for basecalling (NexSeq 500)
The reads in the FASTQ files were aligned to the GRCh38/hg38 human genome (GENECODE 25) with Spliced Transcripts Alignment to a Reference (STAR) version 2.5.2B with default parameters
To assign reads to genes we applied featureCounts.
Genome_build: hg38
Supplementary_files_format_and_content: FASTQ files; tab-delimited text files including raw counts for each Sample.

source_name: KMS11 cell line

growth_protocol: RMPI-1640 medium supplemented with 20% FBS, 1% Penicillin/Streptomycin and 2% HEPES

extract_protocol:
Dynabeads mRNA DIRECT Purification Kit (Thermo Fisher Scientific).
Protocol reproduced from: Jaitin, D. A. et al. (2014) ‘Massively parallel single-cell RNA-seq for marker-free decomposition of tissues into cell types.’, Science, 343(6172), pp. 776–9.

treatment_protocol: shRNA expression was induced by adding 1 μg/ml doxycycline (Sigma) to the culturing media, and replaced every 48 hours. Cells were harvested after 4 days of shRNA expression induction.

tag: genotype/variation


title: KMS11_shPRDM5_2i

description: KMS11 cell line infected with the shRNA#2 targeting PRDM5 prior to shRNA expression induction


title: CE909: TRIM28KO_PolII_N20_1

data_processing:
All sequencing reads were aligned to the mm10 genome assembly using Bowtie2 (allowing 2 mismatches, keeping uniquely aligned reads only).
Genome_build: mm10

source_name: Trim28 KO

extract_protocol:
Lysates were clarified from sonicated nuclei and Polymerase II-DNA complexes were isolated with antibody.
At least 1ng of ChIP DNA was used to prepare sequencing library with Illumina ChIP Sample Library Prep Kit (Illumina, USA) followed by 12 cycles of PCR amplification. Barcoded libraries from different samples were pooled together and sequenced on Illumina HiSeq2000 platform in paired-end sequencing runs.

treatment_protocol: No treatment

tag: strain

value: Trim28 KO

tag: chip antibody

value: sc-899 Pol II (N-20) lot number H3115


title: CE908: WT_PolII_N20_2


title: MitoT- sample 2


title: CE906: TRIM28KO_input_2


title: CE907: WT_PolII_N20_1


title: Naive_KO_REP1


title: Th17_WT_REP2


title: Naive_WT_REP3


title: Treg_WT_REP2


title: KMS11_shPRDM5_2iD

description: KMS11 cell line infected with the shRNA#2 targeting PRDM5 4 days after shRNA expression induction


title: Th1_WT_REP3


title: CE904: WT_input_2


title: Th1_WT_REP2


title: MitoT- sample 3


title: CE905: TRIM28KO_input_1


title: CE903: WT_input_1


title: KMS11_shPRDM5_1iD

description: KMS11 cell line infected with the shRNA#1 targeting PRDM5 4 days after shRNA expression induction


title: Sorted Blimp1+ plasma cells [1030825]

city: Tarrytown

first: Wei Keat

last: Lim

address: 777 Old Saw Mill River Rd

institute: Regeneron Pharmaceuticals

description: 1030825_1_1_180605_D00376_0400_ACC3V3ACXX_L2

data_processing:
FASTQ files were aligned and quantified using Omicsoft ArrayStudio
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text file include read count for each sample

source_name: Sorted Blimp1+ plasma cells

extract_protocol:
Total RNA was purified using MagMAX™-96 Total RNA Isolation Kit (Ambion by Life Technologies) according to manufacturer’s specifications. Genomic DNA was removed using RNase-Free DNase Set (Qiagen).
Strand-specific RNA-seq libraries were prepared using KAPA stranded mRNA-Seq Kit (KAPA Biosystems).

tag: strain background

tag: age

value: 10-12 weeks

value: Blimp-1mCherry reporter

value: Bone Marrow

value: Sorted Blimp1+ plasma cells


title: Sorted CD138+ plasma cells [861786]

description: 861786_1_1_160805_SN390_1040_BC9A21ACXX_L6

source_name: Sorted CD138+ plasma cells

value: Sorted CD138+ plasma cells


title: Th2_KO_REP3

value: CD4 T cells


title: Naive_WT_REP2

value: wild-type


title: Treg_KO_REP2


title: PRRSV_25

city: Urbana

first: Anna

middle: C

last: Dilger

state: Il

address: 1503 S Maryland Ave

department: Animal Sciences

institute: University of Illinois

data_processing:
Adaptors removed using Trim galore v3, sequences less than 20bp removed
Bismark Bisulfite Mapper v0.15.0 and Bowtie2 v2.2.2 to align samples to Ssc10.2 genome, make methylation calls, and extract methylation information
Prepped data for methylkit analysis using command awk ‘{OFS=”\t”;if($4+0>0||$5+0>0) print $1,$2,$3,$4/($4+$5),$4+$5;}’ cytosineReport.txt > outputformethylkit
Genome_build: Ssc10.2
Supplementary_files_format_and_content: tab delimited file providing bisulfite conversion info for cytosines in CpGs; column1=chr, col2=loci, col3=strand, col4=freqC, col5=coverage

organism: Sus scrofa

source_name: PRRSV_LD muscle

extract_protocol:
Genomic DNA was extracted using a standard salting out protocol.
Libraries were prepared with NuGEN Ovation RRBS Methyl-seq kit and prepped for Illumina sequencing.

treatment_protocol: Gilts were intranasally inoculated with either PRRSV or sterile culture medium at 80d gestation. Samples were taken from uninfected male offspring at birth.

tag: maternal infection

value: with sterile culture medium at 80d gestation

tag: sample type

value: uninfected offspring at birth

tag: gender

value: male

value: LD muscle


title: PRRSV_26


title: PRRSV_23


title: Th2_WT_REP2


title: Th17_KO_REP2


title: KO3_0h


title: Th2_KO_REP2


title: Th0_KO_REP2


title: Th1_KO_REP2


title: iPS-MSCs-3

city: Singapore

first: Tongming

last: Liu

address: 60 Biopolis street

department: Cancer stem group

country: Singapore

institute: Genome Institute of Singapore

description:
replicate 3
9271668040_I

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with Genespring

source_name: iPS-MSC

label_protocol: Biotinylated cRNA were prepared with the Ambion Illumina TotalPrep RNA Amplication kit.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit.

tag: cell type

value: iPS-MSC


title: BMSC-3

description:
replicate 3
9271668040_L

source_name: BMSC

value: BMSC


title: PRRSV_22


title: d14-3

description:
replicate 3
9271668040_F

source_name: intermediate

value: intermediate


title: iPS-MSCs-1

description:
replicate 1
9271668040_G


title: PRRSV_20


title: d14-2

description:
replicate 2
9271668040_E


title: Th17_KO_REP1


title: d10-3

description:
replicate 3
9271668040_C

source_name: mesoderm

value: mesoderm


title: BMSC-1

description:
replicate 1
9271668040_J


title: d14-1

description:
replicate 1
9271668040_D


title: Treg_KO_REP1


title: d10-2

description:
replicate 2
9271668040_B


title: d10-1

description:
replicate 1
9271668040_A


title: Th2_KO_REP1


title: BMSC-2

description:
replicate 2
9271668040_K


title: PRRSV_19


title: d8-3

description:
replicate 3
9269325095_L


title: Th1_KO_REP1


title: d8-2

description:
replicate 2
9269325095_K


title: PRRSV_16


title: iPS-MSCs-2

description:
replicate 2
9271668040_H


title: PRRSV_18


title: Treg_WT_REP1


title: Th17_WT_REP1


title: d8-1

description:
replicate 1
9269325095_J


title: d2-3

description:
replicate 3
9269325095_I

source_name: primitive streak

value: primitive streak


title: d2-1

description:
replicate 1
9269325095_G


title: MRC5 iPS d0 rep1

description:
replicate 1
9269325095_D

source_name: iPS

value: iPS


title: control_51

source_name: control_LD muscle

value: with PRRSV at 80d gestation


title: Th2_WT_REP1


title: MRC5 iPS d0 rep3

description:
replicate 3
9269325095_F


title: MRC5  rep3

description:
replicate 3
9269325095_C

source_name: Fibroblast

value: Fibroblast


title: MRC5 iPS d0 rep2

description:
replicate 2
9269325095_E


title: d2-2

description:
replicate 2
9269325095_H


title: control_52


title: control_49


title: control_46


title: control_43


title: Th0_WT_REP1


title: yQC16_Galactose_rep3

city: Pasadena

first: Paul

middle: W

last: Sternberg

state: CA

address: 1200 E California Blvd

department: BBE

institute: Caltech

description:
21067
Total mRNA

data_processing:
Base calls were performed with RTA 1.13.48.0.
Conversion to FASTQ with bcl2fastq 1.8.4.
RNA-seq quantification was performed using Kallisto (Bray et al., 2016) with 200 bootstraps in single-end mode with average length of 300 bp and standard deviation of 20 bp.
Genome_build: YeastEnsemblcDNAR64
Supplementary_files_format_and_content: *_abundance.tsv: Tab-delimited text files with TPM values for each transcript (output from Kallisto quantification).

organism: Saccharomyces cerevisiae

source_name: Diploid cells

growth_protocol: Exponentially growing cells in Synthetic Complete Media 2% Raffinose 30C with Shaking. Around 5e6 to 1e7 cells per ml.

extract_protocol:
Cells were lysed by bead beating on a FastPrep-24 machine using Zymo Quick-RNA Fungal/Bacterial Microprep Kit (Catalog # R2010).
RNA integrity was assessed using RNA 6000 Pico Kit for Bioanalyzer (Agilent Technologies #5067-1513) and mRNA was isolated using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB #E7490). RNA-seq libraries were constructed using NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB #E7770) following manufacturer’s instructions. Briefly, mRNA isolated from ~1 μg of total RNA was fragmented to the average size of 200 nt by incubating at 94 °C for 15 min in first strand buffer, cDNA was synthesized using random primers and ProtoScript II Reverse Transcriptase followed by second strand synthesis using NEB Second Strand Synthesis Enzyme Mix. Resulting DNA fragments were end-repaired, dA tailed and ligated to NEBNext hairpin adaptors (NEB #E7335). After ligation, adaptors were converted to the ‘Y’ shape by treating with USER enzyme and DNA fragments were size selected using Agencourt AMPure XP beads (Beckman Coulter #A63880) to generate fragment sizes between 250 and 350 bp. Adaptor-ligated DNA was PCR amplified followed by AMPure XP bead clean up. Libraries were quantified with Qubit dsDNA HS Kit (ThermoFisher Scientific #Q32854) and the size distribution was confirmed with High Sensitivity DNA Kit for Bioanalyzer (Agilent Technologies #5067- 4626). Libraries were sequenced on Illumina HiSeq2500 in single read mode with the read length of 50 nt following manufacturer's instructions.

treatment_protocol: 2 hours of 2% Galactose or blank (H2O) induction.

value: BY4743 with 14x PP7 at 5' GAL10, short CTD with 10 heptad repeats plus TAF15 low complexity domain.

tag: treatment

value: Galactose


title: yQC16_Galactose_rep2

description:
21059
Total mRNA


title: yQC16_Galactose_rep1

description:
21051
Total mRNA


title: yQC16_NoGalactose_rep3

description:
21063
Total mRNA

value: No Galactose


title: Th1_WT_REP1

source_name: wild-type

value: CD4 T cells


title: yQC16_NoGalactose_rep1

description:
21047
Total mRNA


title: MRC5  rep2

description:
replicate 2
9269325095_B


title: yQC16_NoGalactose_rep2

description:
21055
Total mRNA


title: MRC5  rep1

description:
replicate 1
9269325095_A


title: yQC15_Galactose_rep1

description:
21050
Total mRNA

value: BY4743 with 14x PP7 at 5' GAL10, short CTD with 10 heptad repeats plus FUS low complexity domain.


title: yQC15_NoGalactose_rep3

description:
21062
Total mRNA


title: control_1


title: yQC15_NoGalactose_rep2

description:
21054
Total mRNA


title: yQC15_NoGalactose_rep1

description:
21046
Total mRNA


title: RKO_BCL9_KO_PolyI:C_3

city: brookline

first: Ruben

last: Carrasco

state: MASSACHUSETTS

address: 450 brookline ave

department: Pathology Oncology

institute: dana farber cancer institute

data_processing:
the first 10 bases were trimmed for each read. STAR software was used to map the readings to the human genome (hg19)
duplicates were removed using Picard
HTSeq was used to evaluate the gene expression levels by the count number for each gene and were subsequently annotated using the Ensemble database
Gene differential analysis was then applied to the expression profiling table using R package edgeR
For further analysis, the difference in exon usage between different conditions was calculated and R package DEXSeq was used to find differences between them
Genome_build: hg19
Supplementary_files_format_and_content: Counts Per Kilobase Million CPM

source_name: RKO

growth_protocol: RKO cells were cultured in T75 flask according to ATCC protocol

extract_protocol:
RNA was extracted from wild type and BCL9 knockout RKO cells with or without Poly I:C treatment (1μg/ml) and subsequently purified using the TURBO DNA-free™ Kit (AM1907, invitrogen) to remove any residual DNA
RNA library was prepared using the ribosome RNA removing method and sequenced with a 150bp paired-end protocol in the Center for Cancer Computational Biology at the Dana Farber Cancer Institute
ribosome free RNA seq

value: Colorectal cancer cell line RKO

tag: cell line

value: RKO

value: poly I:C


title: yQC15_Galactose_rep3

description:
21066
Total mRNA


title: control_9

value: uninfected offspring at birth

value: male

value: LD muscle


title: yQC15_Galactose_rep2

description:
21058
Total mRNA


title: control_38


title: yQC7_Galactose_rep3

description:
21065
Total mRNA

value: BY4743 with 14x PP7 at 5' GAL10, short CTD with 10 heptad repeats


title: yQC7_Galactose_rep2

description:
21057
Total mRNA


title: yQC7_Galactose_rep1

description:
21049
Total mRNA


title: RKO_BCL9_KO_PolyI:C_2


title: RO_stim_6hr_SS3

city: Little Rock

first: Henry

last: Wong

state: Arkansas

address: 4301 W. Markham St.

department: Dermatology

institute: University of Arkansas for Medical Science

description:
Gene expression of 6 hr stimulated CD4+CD45RO+ T cells from Sezary syndrome
SS3_6hr

hyb_protocol: Affymetrix HG U133 Plus 2.0 microarrays were hybridized at 45 degrees Celcius for 16 hours.  Hybridized arrays were washed and stained on an Affymetrix GeneChip Fluidics Station 450.

scan_protocol: Microarrays were scanned with an Affymetrix GeneChip scanner 3000

data_processing: All analyses were performed using R version 3.4.  CEL files from both data sets that passed quality control were background corrected and normalized individually using the frozen robust multiarray analysis (fRMA) method. fRMA performs well when microarray data is preprocessed individually because quantile normalization is performed using a reference distribution created from a training database of 850 biologically diverse samples from public repositories.

source_name: Sezary, CD4+CD45RO+ T cells, 6hr stimulated

label_protocol: Biotinylated cRNA was prepared using the Affymetrix GeneChip IVT labeling kit, as directed.

growth_protocol: CD4+CD45RO+ T cells were isolated from PBMCs by negative selection, and rested overnight in RPMI medium supplemented with 10% FBS and 1% PenStrep prior to stimulation.

extract_protocol: Total RNA was purified using Trizol reagent, as directed.

treatment_protocol: Rested T cells were stimulated with PMA + A23187 for 0, 2, and 6 hours.  The 6hr time point is not available for Sezary patient 2.

tag: disease

value: Sezary

value: CD4+CD45RO+ T cells

tag: time point

value: 6hr stimulated

value: blood


title: RO_rest_0hr_SS3

description:
Gene expression of resting CD4+CD45RO+ T cells from Sezary syndrome
SS3_0hr

source_name: Sezary, CD4+CD45RO+ T cells, 0hr resting

value: 0hr resting


title: RO_stim_2hr_SS2

description:
Gene expression of 2 hr stimulated CD4+CD45RO+ T cells from Sezary syndrome
SS2_2hr

source_name: Sezary, CD4+CD45RO+ T cells, 2hr stimulated

value: 2hr stimulated


title: yQC7_NoGalactose_rep3

description:
21061
Total mRNA


title: yQC7_NoGalactose_rep2

description:
21053
Total mRNA


title: RO_stim_2hr_SS3

description:
Gene expression of 2 hr stimulated CD4+CD45RO+ T cells from Sezary syndrome
SS3_2hr


title: RO_rest_0hr_SS2

description:
Gene expression of resting CD4+CD45RO+ T cells from Sezary syndrome
SS2_0hr


title: yQC7_NoGalactose_rep1

description:
21045
Total mRNA


title: RKO_wild_type_PolyI:C_3

tag: genotype

value: wild type


title: RKO_wild_type_PolyI:C_2


title: RO_stim_2hr_SS1

description:
Gene expression of 2 hr stimulated CD4+CD45RO+ T cells from Sezary syndrome
SS1_2hr

tag: tissue


title: RO_stim_6hr_SS1

description:
Gene expression of 6 hr stimulated CD4+CD45RO+ T cells from Sezary syndrome
SS1_6hr


title: WT_Galactose_rep3

description:
21064
Total mRNA

value: BY4743 with 14x PP7 at 5' GAL10 (w/o KAN)

value: Galactose


title: WT_Galactose_rep2

description:
21056
Total mRNA


title: RO_rest_0hr_SS1

description:
Gene expression of resting CD4+CD45RO+ T cells from Sezary syndrome
SS1_0hr


title: WT_Galactose_rep1

description:
21048
Total mRNA


title: RKO_wild_type_PolyI:C_1


title: RKO_BCL9_KO_PolyI:C_1


title: RKO_BCL9_KO_3


title: 181207_BRU3GFP3P90A_IFN

city: Seattle

first: Molly

last: Ohainle

state: WA

address: 1100 Fairview Ave N, C2-023

institute: Fred Hutchinson Cancer Research Center

data_processing:
Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18 software, followed by generation of  fastq files using Illumina's bcl2fastq Conversion Software v1.8.4 (http://support.illumina.com/downloads) /bcl2fastq_conversion_software_184.html).
Reads of low quality were filtered out prior to demultiplexing  using FASTX-Toolkit v0.0.13
Reads were trimmed and aligned to the PIKA HIV guide library using Bowtie v1.0.0, allowing 0 mismatches in the guide sequence, followed by tabulation of read counts using R
Genome_build: PIKA HIV sgRNA Library
Supplementary_files_format_and_content: tab delimited files with read counts for each guide sequence

organism: Human immunodeficiency virus

source_name: Human Immunodeficiency Virus (HIV)

growth_protocol: ZAP-KO THP-1 monocytic cells are grown in RPMI with 10% FBS and Pen/Strep (supplemented to 10mM HEPES, 4.5 g/L D-Glucose, 0.11 g/L Sodium Pyruvate + Glutamax), passaging between 2 x 10^5 cells/mL and 1 x 10^6 cells/mL.

extract_protocol:
Viral RNA was extracted using a QIAamp Viral RNA Mini Kit (Qiagen)
described in samples section individually for each sample
Genomic DNA or reverse-transcribed viral RNA were amplified by a two-step PCR (PCR1: 12 cycles, PCR2: 20 cycles) to amplify 20bp sgRNA sequences in the HIV-CRISPR vector. All Viral RNA was amplified for each sample where appropriate. For Genomic DNA samples a total of 500-fold coverage of the 15,414 sgRNAs were amplified (10^6 cells were estimated to contain 6.6μg gDNA) with a maximum of 2μg gDNA per PCR reaction. For each sample, PCR1 reactions were pooled, cleaned up over a QIAquick PCR purification Kit (2 columns per sample), pooled again and used as template for PCR2. For viral RNA, all PCR1 was amplified in the second round. For gDNA, 5uL of pooled PCR1 was used as input for PCR2 (PCR2 primers include Illumina barcodes and adaptor sequences). Amplicons from PCR2 were pooled, purified by double-sided SPRI (AMPureXP, Beckman Coulter), quantified with a Qubit HS dsDNA assay and pooled for sequencing.

treatment_protocol: 8 x 10^6 cells (>500X coverage) were transduced with the PIKAHIV library (MOI of 0.75) and selected in 1ug/mL puromycin for 10-14 days. For each replicate, 8 x 10^6 cells were infected with or without overnight IFNα treatment with HIV. Cells and viral supernatants were harvested 3 days post-infection.

value: ZAP-KO THP-1

tag: ifn treatment

value: yes

tag: molecule

value: viral RNA


title: RKO_BCL9_KO_2

value: Colorectal cancer cell line RKO

value: RKO


title: WT_NoGalactose_rep2

description:
21052
Total mRNA

tag: genotype/variation

value: No Galactose


title: 181207_BRU3GFP3N74D_noIFN

value: no


title: RKO_BCL9_KO_1


title: 180911_BRU3GFP3WT_IFN_vRNA_2


title: RO_stim_2hr_ND3

description:
Gene expression of 2 hr stimulated CD4+CD45RO+ T cells from normal donor
ND3_2hr

source_name: normal, CD4+CD45RO+ T cells, 2hr stimulated

value: normal


title: RKO_wild_type_3


title: 180911_BRU3GFP3WT_IFN_vRNA_1


title: RKO_wild_type_2


title: WT_NoGalactose_rep3

description:
21060
Total mRNA

tag: strain


title: RKO_wild_type_1


title: RO_rest_0hr_ND3

description:
Gene expression of resting CD4+CD45RO+ T cells from normal donor
ND3_0hr

source_name: normal, CD4+CD45RO+ T cells, 0hr resting


title: CE910: TRIM28KO_PolII_N20_2

source_name: Trim28 KO

value: Trim28 KO

value: CD4 T cells

tag: chip antibody

value: sc-899 Pol II (N-20) lot number H3115


title: 180911_BRU3GFP3N74D_IFN_vRNA_2


title: WT_NoGalactose_rep1

description:
21044
Total mRNA


title: RO_stim_6hr_ND3

description:
Gene expression of 6 hr stimulated CD4+CD45RO+ T cells from normal donor
ND3_6hr

source_name: normal, CD4+CD45RO+ T cells, 6hr stimulated

value: CD4+CD45RO+ T cells

value: 6hr stimulated

value: blood


title: RO_stim_6hr_ND2

description:
Gene expression of 6 hr stimulated CD4+CD45RO+ T cells from normal donor
ND2_6hr


title: RO_rest_0hr_ND2

description:
Gene expression of resting CD4+CD45RO+ T cells from normal donor
ND2_0hr

value: 0hr resting


title: D-MH-RP-2

status: Public on Nov 15 2019

city: Beijing

first: Qi

state: Beijing

address: Dong xiaofu No 1, Xiangshan Road, Haidian District

department: State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry

country: China

institute: Chinese Academy of Forestry

description: Phloem biological replicate2

data_processing:
Illumina Casava1.7 software used for basecalling.
Cutadapt (v1.18) in python (v2.7) is used to sequentially trim 5’ and 3’ adapters from raw reads of FASTQ file. FASTX-Toolkit is then utilized to trim and filter reads with low quality (Q20 in default).
After adaptor trimming, low quality filtering and contamination checking, the clean sequencing data are mapped to a reference genome using Bowtie (v1.2.2) (http://bowtie-bio.sourceforge.net).A maximum of one mismatch (-v 1) was allowed, and the best alignments of reads was reported in default.
All clean small RNA reads/tags were mapped against the RNA libraries and the mapped tags are then use to identify and profile sncRNAs.
Genome_build: Pop_tri_v3
Supplementary_files_format_and_content: counts

organism: Populus deltoides

source_name: Phloem

growth_protocol: Samples were collected from 7-yr-old poplar (Populus deltoides) trees growing at a nursery in Fangshan (Beijing, China). The sampled trees represented clonal copies of genotype ‘CAF001’. Wood pieces were collected from three replicate trees at the beginning of August 2017. All samples were collected at noon.

extract_protocol:
Total RNA was isolated by standard TRIzol protocol. For RNA quality examination, RNA purity was checked using the kaiaoK5500®Spectrophotometer (Kaiao, Beijing, China) while RNA integrity and concentration was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA). For library preparation for small RNA sequencing, total RNA was separated by 15% agarose gels to extract the small RNA (18-30 nt). After precipitated by ethanol and centrifugal enrichment of small RNA sample, the library was prepared according to the method and process of Small RNA Sample Preparation Kit (Illumina, RS-200-0048). The main contents are as follows:1) Connecting the 3' adaptor to the separated small RNA; 2) Connecting the 5' adaptor to the separated small RNA; 3) RT－PCR; 4) Recycling strips of 145-160bp (22-30nt RNA).
RNA concentration of library was measured using Qubit® RNA Assay Kit in Qubit® 2.0 to preliminary quantify and then dilute to 1ng/μl. Insert size was assessed using the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA), and after the insert size consistent with expectations, qualified insert size was accurate quantitative using Taqman fluorescence probe of AB Step One Plus Real-Time PCR system (Library valid concentration>2nM).The qualified libraries were sequenced by an Illumina platform and generate 50bp single-end reads.

treatment_protocol: Samples were taken at breast height in a part of the stem free of branches or traumatic resin ducts. To preserve intact cambium the bark, phloem and part of the wood was removed from a c. 5 cm × 10 cm region around the sampling area using a carpet knife. This released the shearing forces present in the stem. Samples covering bark, phloem, cambium, developing xylem and two to three previous year rings were then taken by hammering a chisel into the stem at a 90° angle immediately above the pieces and hammering tangentially downwards. The samples used for small RNA-seq were immediately frozen in liquid N2 and kept on dry ice until storage at -80°C.

value: Phloem


title: RO_stim_2hr_ND2

description:
Gene expression of 2 hr stimulated CD4+CD45RO+ T cells from normal donor
ND2_2hr

value: 2hr stimulated


title: D-MH-CM-2

description: Xylem biological replicate2

source_name: Xylem

value: Xylem


title: D-MH-Y-2

description: Leaf biological replicate2

source_name: Leaf

value: Leaf


title: 180911_BRU3GFP3N74D_IFN_vRNA_1

value: ZAP-KO THP-1

value: yes

value: viral RNA


title: ES-2 cells 1

city: Lanzhou

first: Wang

last: Hui

state: Gansu

address: QIlihe, Jiangouyan, NO.335

institute: Chinese Academy of Agricultural Scien

description: Gene expression data from human ovarian cancer ES-2 cell lines

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: Human ovarian cancer cell lines

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: ES-2 cells were cultured to logarithmic growth stage

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Total RNA was extracted using Trizol solution (GibcoBRL)

value: ES-2 cells


title: D-MH-CM-1

description: Xylem biological replicate1


title: D-MH-XCC-3

description: Cambium biological replicate3

source_name: Cambium

value: Cambium


title: D-MH-Y-1

description: Leaf biological replicate1


title: ES-2 cells 2


title: ES-2 cells 3


title: RO_stim_6hr_ND1

description:
Gene expression of 6 hr stimulated CD4+CD45RO+ T cells from normal donor
ND1_6hr

value: normal


title: D-MH-RP-3

description: Phloem biological replicate3


title: D-MH-XCC-1

description: Cambium biological replicate1


title: Biofilm_total_RNA_Rep3

city: Tokyo

first: Kotaro

last: Chihara

address: 1-23-1 Toyama

department: Research Center for Drug and Vaccine Development

country: Japan

institute: National institute of infectious diseases

data_processing:
Total RNA-seq reads in FASTQ format were quality and adapter-trimmed via Cutadapt (Martin, 2011) version 1.15 using a cut-off Phred score of 20 in NextSeq mode and reads without any remaining bases were discarded (command line parameters: --nextseq-trim=20 -m 1 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC)
Remaining reads longer than 11 nt were aligned to the P. aeruginosa reference genomes (NC_002516) using READemption version 0.4.5 (Förstner et al., 2014) and segemehl (Hoffmann et al., 2014) version 0.2.0 with accuracy cut-off of 95%
Each read with a minimum overlap of 1 nt was counted with a value based on the number of locations where the read was mapped using READemption (Förstner et al., 2014). If the read overlapped more than one annotation, the respective value was counted once for each overlapping region.
The resulting read counts were subjected to differential expression analysis of planktonic vs. biofilm samples via DESeq2 version 1.18.1 with parameter for fold-change shrinkage of “betaPrior=TRUE”.
Genome_build: P. aeruginosa genomes (NC_002516)
Supplementary_files_format_and_content: read counts were subjected to differential expression analysis of planktonic vs. biofilm samples via DESeq2 version

organism: Pseudomonas aeruginosa

growth_protocol: For planktonic culture, overnight culture of P. aeruginosa PAO1 strain containing hfq::3xFLAG allele was diluted 1:100 into 200 ml fresh LB medium and maintained up to an OD600 of 2.0. For biofilm condition, 10 μl aliquot of 1:100 diluted overnight culture was seeded on a cellulose membrane placed on the LB agar and incubated statically for 48 hours.

extract_protocol:
Bacteria were lysed and total RNA was purified with hot phenol extraction followed by chloroform extraction and ethanol precipitation.
cDNA preparation and high-throughput sequencing were performed at Vertis Biotechnologie AG, Freising, Germany.

treatment_protocol: Biofilms from the same biological replicate were scraped with sterilized loop into 200 ml LB medium. Cultures which were irradiated with UV light (254 nm, 800 mJ/cm2) were used.

tag: growth condition

value: Biofilm (statically incubated for 48 hours at 37degreeC on LB agar plate)

tag: protocol

value: UV light (254 nm, 800 mJ/cm2) irradiation


title: RO_stim_2hr_ND1

description:
Gene expression of 2 hr stimulated CD4+CD45RO+ T cells from normal donor
ND1_2hr


title: CADM1-overexpression ES-2 cells 2

description: Gene expression data from CADM1-overexpression human ovarian cancer ES-2 cell lines

source_name: CADM2-overexpression Human ovarian cancer cell lines

value: CADM1-overexpression ES-2 cells


title: Planktonic_total_RNA_Rep3

value: Planktonic (LB, 37degreeC, 180 rpm, OD600 = 2.0)


title: D-MH-RP-1

description: Phloem biological replicate1


title: CADM1-overexpression ES-2 cells 1

source_name: CADM1-overexpression Human ovarian cancer cell lines


title: Th0_KO_REP1

value: CD4 T cells


title: D-MH-Y-3

description: Leaf biological replicate3


title: D-MH-XCC-2

description: Cambium biological replicate2


title: Biofilm_total_RNA_Rep2


title: Biofilm_total_RNA_Rep1


title: Planktonic_total_RNA_Rep2


title: Planktonic_total_RNA_Rep1


title: Biofilm_XL-_Rep2

description: Hfq-binding RNA

data_processing:
CLIP-seq reads in FASTQ format were quality and adapter-trimmed via Cutadapt (Martin, 2011) version 1.15/1.16 using a cut-off Phred score of 20 in NextSeq mode and reads without any remaining bases were discarded (command line parameters: --nextseq-trim=20 -m 1 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A GATCGTCGGACTGTAGAACTCTGAACGTGTAGATCTCGGTGGTCGCCGTATCATT)
To eliminate putative PCR duplicates, paired-end reads were collapsed using FastUniq (Xu et al. 2012)
Remaining reads longer than 11 nt were aligned to the P. aeruginosa reference genomes (NC_002516) using READemption version 0.4.5 (Förstner et al., 2014) and segemehl (Hoffmann et al., 2014) version 0.2.0 with accuracy cut-off of 80%
The uniquely mapped reads were used for coverage calculation (Förstner et al., 2014)
Coverage normalization was performed based on DESeq2 size factor (Anders et al., 2010) during peak calling (https://github.com/tbischler/PEAKachu, manuscript in preparation)
Genome_build: P. aeruginosa genomes (NC_002516)
Supplementary_files_format_and_content: wiggle

extract_protocol:
Bacteria were lysed and the FLAG-tagged Hfq was immunoprecipitated using a monoclonal anti-FLAG antibody (Sigma, M8823). The samples were treated with benzonase nuclease (Sigma, E1014), calf intestine phosphatase (NEB, M0290), and polynucleotide kinase (Thermo, EK0032) in the presence of radioactive gamma-ATP. Samples were separated with SDS-PAGE and followed by transfering to nitrocellulose membranes. Radioactively labelled RNA-protein complexes were eluted from membranes and treated with Proteinase K. RNA was purified with phenol:chloroform extraction and ethanol precipitation.
Purified RNA was used as input for library preparation using the NEBNext Small RNA Library kit according to the manufacturer’s instructions.

treatment_protocol: Biofilms from the same biological replicate were scraped with sterilized loop into 200 ml LB medium. Half of each culture was irradiated with UV light (254 nm, 800 mJ/cm2) while the other half was left untreated.

value: none (untreated control)

tag: clip antibody

value: Anti-FLAG M2 monoclonal antibody attached to magnetic beads


title: Biofilm_XL-_Rep1

description: Hfq-binding RNA


title: Biofilm_XL+_Rep3

description: Hfq-binding RNA


title: Biofilm_XL-_Rep3

description: Hfq-binding RNA


title: Planktonic_XL+_Rep2

description: Hfq-binding RNA


title: Planktonic_XL-_Rep1

description: Hfq-binding RNA


title: Planktonic_XL+_Rep1

description: Hfq-binding RNA


title: Planktonic_XL-_Rep3

description: Hfq-binding RNA


title: Biofilm_XL+_Rep1

description: Hfq-binding RNA


title: Biofilm_XL+_Rep2

description: Hfq-binding RNA


title: k_stem_4

city: Atlanta

first: Haydn

last: Kissick

state: Georgia

address: 1462 Clifton Rd

institute: Emory University

data_processing:
Rna samples: Adapter trim with cutadapt, align with StarAligner, counts with Htseqcount, differential expression between groups with DESeq2
DNA methylation: Adapter trim with cutadapt, differentially methylated CpGs identified by fisher exact test compared to each CpGs Naïve cells, Differentially methylated regions identified using custom python analysis finding continuous regions with atleast 5/10 significantly (p=0.0001) differentially methylated CpGs
Genome_build: hg38
Supplementary_files_format_and_content: Counts

extract_protocol:
RNA and DNA was extracted using qiagen all-prep kits
DNA methylation was done using illumina methylseq protocol, Bladder rna libraries  were prepared using Nugen Ovation, Kidney and prostate RNA libraries prepared using clontech smartseq V2

value: Kidney tumor

value: CD8 T-cell

tag: cell subtype


title: p_stem_1

value: prostate tumor


title: Planktonic_XL-_Rep2

description: Hfq-binding RNA


title: Planktonic_XL+_Rep3

description: Hfq-binding RNA


title: p_stem_2


title: CADM1-overexpression ES-2 cells 3

source_name: CADM3-overexpression Human ovarian cancer cell lines


title: RO_rest_0hr_ND1

description:
Gene expression of resting CD4+CD45RO+ T cells from normal donor
ND1_0hr

value: CD4+CD45RO+ T cells

value: 0hr resting

value: blood


title: Th0_WT_REP2

data_processing: Microarray data were carried out with R (version 3.1.0) using packages from the Bioconductor. Raw data CEL files were used and the quality control analysis was performed using ArrayQualityMetrics package. The raw data were preprocessed using the RMA (Robust Multi-array Average) method available in oligo package. Gene expression levels were analyzed on a base-2 logarithmic scale.

source_name: wild-type

value: wild-type


title: k_stem_3


title: k_stem_1


title: k_ef_4


title: k_stem_2


title: k_ef_1


title: k_ef_2


title: CP Dmpk 480/480 rep 3

city: Gainesville

first: Maurice

middle: S

last: Swanson

state: FL

address: 2033 Mowry Road,, Cancer & Genetics Research Complex, Swanson Lab, Room 220G

institute: University of Florida

description:
paired end sequencing
processed data file:
SupplementaryTable3.xlsx

data_processing:
Basecalling was done by Illumina, fastq files were obatined with BaseMount. Fastq files were quality assessed using Fastqc, and filtered or trimmed as necessary.
Reads were aligned to the mm10 genome using STAR.  Alternative Splicing analysis was performed with rMATS4.
The rMATS output was filtered using the R package MASER, using the following settings: average reads >=5, change in percent spliced in (PSI) >= 10%, False Discovery rate =0.05.
Genome_build: mm10
Supplementary_files_format_and_content: processed data files contain the output from the splicing analysis after rMATS and MASER.

source_name: choroid plexus

extract_protocol:
RNA was extracted using Trizol at 55C with mixing for 10 min. After cooling to room temperature, total RNA was extracted using the Direct-zol RNA miniprep kit (Zymo Research), following manufacturer's instructions.
Libraries were made using the NEB Next UltraII Directional RNA library kit with the rRNA depeletion module and sequenced on the NextSeq 500.

value: FVB

tag: mouse number

value: derived from R309

value: choroid plexus


title: CP Dmpk 480/480 rep 2

value: derived from R305


title: CP Dmpk 480/480 rep 1

value: derived from R303


title: CP Dmpk +/480 rep 3

value: derived from R307


title: CP Dmpk +/480 rep 2

value: derived from R304


title: CP Dmpk +/480 rep 1

value: derived from R301


title: CP Dmpk+/+ rep 3

value: derived from R310

value: Dmpk+/+


title: CP Dmpk+/+ rep 2

value: derived from R306


title: CP Dmpk+/+ rep1

value: derived from R302

value: Dmpk+/+ rep1


title: myotube Dmpk 480/480 rep 1

description:
paired end sequencing
processed data file:
SupplementaryTable2.xlsx

source_name: myotube

value: myotube


title: myotube Dmpk 480/480 rep 3


title: myotube Dmpk 480/480 rep 2


title: myotube Dmpk+/+ rep 3


title: myotube Dmpk +/480 rep 2


title: myotube Dmpk+/+ BL6 rep3

description:
paired end sequencing
processed data file:
No processed data provided.

value: derived from P887


title: myotube Dmpk +/480 rep 3


title: myotube Dmpk+/+ rep1


title: myotube Dmpk+/+  BL6 rep1

value: derived from P772


title: k_ef_3

value: Kidney tumor

tag: cell type

value: CD8 T-cell


title: myotube Dmpk 170/170 rep 2

value: derived from P886


title: TA Dmpk 480/480 rep 1

description:
paired end sequencing
processed data file:
SupplementaryTable1.xlsx

source_name: Tibialis anterior

value: FVB

value: Tibialis anterior


title: TA Dmpk +/480 rep 2


title: TA Dmpk +/480 rep 3


title: TA Dmpk 480/480 rep 2


title: TA Dmpk +/480 rep 1


title: TA Dmpk+/+ rep 3


title: TA Dmpk+/+ rep 2


title: TA Dmpk+/+ rep1


title: myotube Dmpk 170/170 rep 1

value: derived from P842


title: Regen_Dmp1CreERT2TdT_14 DPA_scRNA-seq

city: Toronto

first: Freda

middle: D

last: Miller

state: Ontario

address: 686 Bay Street

department: Neurosciences and Mental Health

country: Canada

institute: The Hospital For Sick Children

description: Mice were injected intraperitoneally with 3mg/day of tamoxifen for four consecutive days, digits were then amputated after 10 additional days and the regenerating digit tips distal to the original amputation site were collected at 14 days post amputation. When processing the sequencing data, the reads were aligned to the mm10_TdTomato genome.

data_processing:
FASTQ sequencing reads were processed, aligned to the mouse genome (mm10) and converted to digital gene expression matrices using the Cell Ranger Single Cell Software Suite.
The number of cell barcodes per sample was identified by calculating the cumulative fraction of reads attributable to each individual cell barcode and arranging these in decreasing order.
Genome_build: mm10
Supplementary_files_format_and_content: The data packages contain the filtered digital gene expression for each sample obtained from the Cell Ranger Single Cell Pipeline.

source_name: Adult regenerating digit tip

extract_protocol:
Tissue was dissected from the region of the digit/limb as indicated in the source name, at the specific timepoint indicated in the sample title. Freshly dissected tissue was digested in Liberase (280ug/mL) at 37°C for 1 - 4hr, with constant aggitation. Cells were mechanically dissociated with a small-bore-hole glass pipette, filtered through a 20um cell strainer and pelleted by centrifugation at 1000 rpm for 5 min. The cell pellet was then washed in 1X HBSS and cells were counted with a haemocytometer and pelleted again by centrifugation at 1000 rpm for 5 min. The cell pellet was re-suspended in a solution containing 0.04% BSA in 1X HBSS at a concentration of 500-700 cells/ul, prior to collection of single cell transcriptomes.
Libraries were prepared according to the manufacturer's instructions (10X Genomics) using the Chromium Single Cell 3' Library and Gel Bead Kit.

value: Adult regenerating digit tip

tag: regeneration time point

value: 14 Days

tag: number of digits

tag: age

value: 10 - 12 Weeks

tag: time spent in enzymatic digestion


title: E14_scRNA-seq

source_name: Embryonic digit tips from hindlimbs

value: Embryonic digit tips from hindlimbs

value: 0 Days

value: 23 Embryos; 138 Digit Tips

value: Embryonic Day 14


title: Cxcr4_sgRNA_b_rep_3

city: Lund

first: Marcus

last: Järås

address: Universitetssjukhuset

department: Clinical Genetics

country: Sweden

institute: Lund University

description:
mRNA
processed data file: MLLAF9_CXCR4KD_Day10_FPKM.txt

data_processing:
Bcl2FastQ software was used for basecalling.
The sequenced reads were mapped to mm10 whole genome using STAR aligner, version 2.5.0a.
BAM files were imported to the Qlucore Omics Explorer 3.0 software and normalized using the FPKM (Fragments Per Kilo Million).
Features with less than 5 reads in at least 4 samples were discarded.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: MLLAF9_CXCR4KD_Day10_FPKM.txt: Tab-delimited .txt file of FPKM values, fold change and p-values of t-test between control sgRNAs andCxcr4_sgRNA cells for every gene. A rank was created for each gene based on the log10 of the p-value and the direction of the fold change.

source_name: MLL-AF9 leukemia cells

extract_protocol:
Femurs and tibia of the mice were crushed and the leukemia cells were extracted. The cells were FACS sorted for GFP and RNA was extracted using Qiagen RNeasy kit.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: MLL-AF9 leukemia cells were transduced with control or Cxcr4 sgRNAs and transplanted into sub-lethally irradiated C57BL/6 mice.

value: Bone marrow-derived leukemia cells

tag: sgrna


title: myotube Dmpk +/480 rep 1

value: derived from R301

tag: tissue

value: myotube

tag: genotype


title: myotube Dmpk 170/170 rep 3

value: derived from P917


title: Control_sgRNA_rep_2


title: Control_sgRNA_rep_3


title: Control_sgRNA_rep_4


title: Control_sgRNA_rep_1


title: Cxcr4_sgRNA_b_rep_2


title: Cxcr4_sgRNA_a_rep_3


title: Cxcr4_sgRNA_b_rep_1


title: RykSL/SL lung 2

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

country: Germany

institute: MPI for heart and lung research

data_processing:
The resulting raw reads were assessed for quality, adapter content and duplication rates with FastQC.
Reaper version 15-065 was employed to trim reads after a quality drop below a mean of Q20 in a window of 20 nucleotides.  Only reads between 15 and 75 nucleotides were considered for further analyses.
Trimmed and filtered reads were aligned to the Ensembl mouse genome version mm10 (GRCm38) using STAR 2.4.0a with the parameter “--outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%.
The number of reads aligning to genes was counted with the featureCounts 1.5.1 tool from the Subread package.  Only reads mapping at least partially inside exons were admitted and aggregated per gene.  Reads overlapping multiple genes or aligning to multiple regions were excluded.
Differentially expressed genes (DEGs) were identified using DESeq2 version 1.14.1.  Only genes with a minimum fold change of ±2 (log2 ±1), a maximum Benjamini-Hochberg corrected p-value of 0.05, and a minimum combined mean of 5 reads were considered to be significantly differentially expressed.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include library size normlized counts

source_name: Postnatal day 1 lung (left lobe)

growth_protocol: mouse postnatal day 1 lungs

extract_protocol:
Total RNA was isolated from P1 lungs (left lobes) of two wild-type and two RykSL/SL mice using Trizol (Life Technologies) combined with on-column DNase digestion (TURBO DNAse, Ambion) to avoid contamination by genomic DNA.
3 µg of total RNA was used as input for Truseq Stranded mRNA Library preparation following the low sample protocol (Illumina).

treatment_protocol: no treatment

value: Postnatal day 1

value: lung (left lobe)

value: RykSL/SL


title: TA Dmpk 480/480 rep 3

value: FVB


title: Cxcr4_sgRNA_a_rep_2


title: wild-type lung 1

value: wild-type


title: Cxcr4_sgRNA_a_rep_1


title: wild-type lung 2


title: RykSL/SL lung 1


title: Uninjured_2_scRNA-seq

description: Cells isolated from the second uninjured digit tip sample were digested with 0.25% collagenase, type 1 for 1hr and a further 3hr with Liberase at 37°C in order to liberate bone-associated cells.

source_name: Adult distal digit tip

value: Adult distal digit tip


title: Non_Regen_10_2 DPA_scRNA-seq

source_name: Adult non-regenerative mesenchymal cap

value: Adult non-regenerative mesenchymal cap

value: 10 Days


title: 151307032_5hmC_Seal

city: Chicago

first: Wei

last: Zhang

state: IL

address: 680 N Lake Shore Drive, Suite 1400

department: Preventive Medicine

institute: Northwestern University

description: Sex: 1; male

data_processing:
library strategy: 5hmC-Seal (selective 5hmC chemical labeling)
raw sequencing reads were trimmed for adaptor sequences using Trimmomatic
Low quality bases were also trimmed to a minimum length of 30 bp, followed by alignment to the current human genome reference (hg19) using Bowtie2 [24] with the end-to-end alignment mode,Read pairs were concordantly aligned with fragment length ≤ 500 bp and with average ≤ 1 ambiguous base and up to four mismatched bases per 100 bp length.
Alignments with Mapping Quality Score ≥ 10 were counted for gene bodies, according to the gene start and gene end annotations by the GENCODE Project [25](release 19), using featureCounts [26] without strand information.
peaks were called using PeaksFind version 2.2 with the following setting: ChIP threshold (0.2), Enrichment Fold (2.5), Rescue Fold (3).
The 5hmC-Seal libraries were sequenced to produce a median number of ~25 million reads in cfDNA samples, and a median number of ~13.5 million unique reads (~55% of total reads) were mapped to the ~22,000 gene body regions.
Genome_build: hg19

source_name: Plasma

extract_protocol:
Approximately 2-3 mL of frozen plasma from each subject was processed by centrifuging at 1,350 × g for 12 min twice, then at 13,500 × g for 12 min once, and followed by cfDNA extraction (1-2 ng/sample) using the QIAamp Circulating Nucleic Acid Kit (Qiagen, Germany). Genomic DNA (gDNA) from cfDNA-paired tumor blocks for 7 patients were isolated (30-50 ng/sample) using the Qiagen DNeasy Blood and Tissue Kit (Qiagen, Germany) and fragmented by sonication.
We constructed 5hmC-Seal libraries according to established protocol.22 DNA samples were first repaired and ligated with adaptors. Next, the T4 bacteriophage enzyme β-glucosyltransferase was used to transfer an engineered glucose moiety containing an azide-group to 5hmC in duplex DNA. A biotin tag was then added to the azide group using Huisgen cycloaddition (“Click”) chemistry. Finally, the 5hmC-containing DNA fragments with biotin tags were captured by avidin beads. The 5hmC-Seal libraries were constructed through PCR amplification and sequenced using the Illumina NextSeq500 platform (PE38) at the University of Chicago Genomics Core Facility. We randomized all samples when preparing the 5hmC-Seal libraries and sequencing. Technical robustness, including reproducibility, of the 5hmC-Seal was demonstrated in our previous report

tag: subject status

value: newly diagnosed patients with DLBCL

tag: race

value: Blk

tag: Sex

value: male

tag: dlbcl tumor stage

value: GCB

tag: ldh

tag: deaths=0; alive=1

tag: follow-up time for death (months)

tag: event

value: 1; relapse or death

tag: follow-up time for event (months)

value: Plasma

tag: molecule subtype

value: circulating cell-free DNA (cfDNA)


title: 151212005_5hmC_Seal

description: Sex: 1; male

value: Wht

value: ABC


title: 151201027_5hmC_Seal

description: Sex: 0; female

value: female


title: myotube Dmpk+/+ rep 2

tag: strain

tag: mouse number

value: derived from R306

value: myotube

value: Dmpk+/+


title: Cxcr4_sgRNA_a_rep_4

tag: cell type

value: Bone marrow-derived leukemia cells


title: 151310006_5hmC_Seal

description: Sex: 0; female

tag: age

value: 0; no relapse and death


title: 151007049_5hmC_Seal

description: Sex: 1; male


title: 151105079_5hmC_Seal

description: Sex: 0; female


title: 151109089_5hmC_Seal

description: Sex: 1; male


title: 151110135_5hmC_Seal

description: Sex: 1; male


title: siSP1 for siSP1 knockdown in human in vitro differentiated adipocyte_rep 3

city: Stockholm

first: Simon

last: Lecoutre

address: Huddinge

department: MedH

institute: Karolinska Institutet

description:
SP1_siSp1_3
Gene expression data of human in vitro differentiated adipocyte day 13 treated with siSP1 at day 9.

hyb_protocol: Hybridization, washing and staining were carried out on Clariom D Human arrays, using Affymetrix GeneChip Fluidics Station 450 according to the manufacturer’s protocol.

scan_protocol: The fluorescent intensities were determined with Affymetrix GeneChip Scanner 3000 7G, and Affymetrix GeneChip Command Console (AGCC, v.4.1.2) was used to analyze the acquired array images.

data_processing:
Gene-level SST-RMA processing and sample group comparisons were performed using Transcriptome Analysis Console (TAC, v.4.0).
Nominally significant genes (p<0.01) were analysed in a gene ontology (GO) analysis performed using an online web tool (https://david.ncifcrf.gov/).

label_protocol: Biotinylated DNA targets was prepared from 150 ng total RNA using the GeneChip WT Plus Reagent Kit according to the manufacturer's instructions.

growth_protocol: Cultures of in vitro differentiated human adipocytes were set up and differentiated in media containing a standard differentiation adipogenic cocktail; 5 mg/ml insulin, 0.25 mmol/l dexamethasone, 0.5 mmol/l 3-isobutyl-1-methylxanthine (IBMX) and 10 mmol/l rosiglitazone for two days after which the dexamethasone and IBMX were removed and the cells were allowed to undergo full adipogenic differentiation.

extract_protocol: Total RNA was extracted from human in vitro differentiated adipocyte. RNA quantity was measured using NanoDrop ND-1000 Spectrophotometer.

treatment_protocol: Human in vitro differentiated adipocyte day 13 treated with siSP1 or siC at day 9 (SP1-regulated transcriptome) or human in vitro differentiated adipocyte day 11 treated with 0.5 mM (L) or 10 mM (H) of glutamine during differentiation.

value: in vitro differentiated adipocyte

tag: treatment


title: 151308042_5hmC_Seal

description: Sex: 0; female

tag: tissue


title: siSP1 for siSP1 knockdown in human in vitro differentiated adipocyte_rep 2

description:
SP1_siSp1_2
Gene expression data of human in vitro differentiated adipocyte day 13 treated with siSP1 at day 9.


title: siControl for siSP1 knockdown in human in vitro differentiated adipocyte_rep 2

description:
SP1_sicontrol_2
Gene expression data of human in vitro differentiated adipocyte day 13 treated with sicontrol at day 9.

value: siControl


title: siSP1 for siSP1 knockdown in human in vitro differentiated adipocyte_rep 1

description:
SP1_siSp1_1
Gene expression data of human in vitro differentiated adipocyte day 13 treated with siSP1 at day 9.


title: 151308037_5hmC_Seal

description: Sex: 1; male

value: newly diagnosed patients with DLBCL


title: 151312033_5hmC_Seal

description: Sex: 1; male


title: 151401015_5hmC_Seal

description: Sex: 1; male


title: siControl for siSP1 knockdown in human in vitro differentiated adipocyte_rep 3

description:
SP1_sicontrol_3
Gene expression data of human in vitro differentiated adipocyte day 13 treated with sicontrol at day 9.


title: 151403015_5hmC_Seal

description: Sex: 0; female


title: siControl for siSP1 knockdown in human in vitro differentiated adipocyte_rep 1

description:
SP1_sicontrol_1
Gene expression data of human in vitro differentiated adipocyte day 13 treated with sicontrol at day 9.


title: 151308021_5hmC_Seal

description: Sex: 0; female


title: 171102061_5hmC_Seal

description: Sex: 1; male


title: myotube Dmpk+/+ BL6 rep2

value: derived from P773

tag: genotype


title: 151403045_5hmC_Seal

description: Sex: 0; female

tag: subject status


title: 151207041_5hmC_Seal

description: Sex: 1; male

tag: race

value: male


title: 151305019_5hmC_Seal

description: Sex: 1; male

tag: Sex

value: GCB


title: 151204012_5hmC_Seal

description: Sex: 1; male

tag: dlbcl tumor stage


title: 151303040_5hmC_Seal

description: Sex: 0; female

tag: ldh


title: 151109084_5hmC_Seal

description: Sex: 1; male

tag: deaths=0; alive=1


title: 151202070_5hmC_Seal

description: Sex: 1; male

tag: follow-up time for death (months)


title: 151309027_5hmC_Seal

description: Sex: 1; male

tag: event


title: 151109044_5hmC_Seal

description: Sex: 1; male

tag: follow-up time for event (months)


title: 151108070_5hmC_Seal

description: Sex: 1; male

tag: molecule subtype


title: 151302016_5hmC_Seal

description: Sex: 0; female


title: 151206013_5hmC_Seal

description: Sex: 0; female


title: 151106086_5hmC_Seal

description: Sex: 1; male

value: 1; relapse or death


title: 151305010_5hmC_Seal

description: Sex: 0; female

value: Blk

value: Plasma


title: 151202008_5hmC_Seal

description: Sex: 1; male

value: circulating cell-free DNA (cfDNA)


title: 151106004_5hmC_Seal

description: Sex: 0; female

value: Wht


title: 151106023_5hmC_Seal

description: Sex: 1; male


title: 151210021_5hmC_Seal

description: Sex: 0; female

value: female


title: 151106045_5hmC_Seal

description: Sex: 1; male


title: 151009030_5hmC_Seal

description: Sex: 1; male


title: 151009031_5hmC_Seal

description: Sex: 0; female


title: 151010045_5hmC_Seal

description: Sex: 1; male

value: ABC


title: 151105046_5hmC_Seal

description: Sex: 1; male


title: 151102056_5hmC_Seal

description: Sex: 1; male


title: 151006052_5hmC_Seal

description: Sex: 1; male


title: 151101047_5hmC_Seal

description: Sex: 1; male

value: H/L


title: 151008048_5hmC_Seal

description: Sex: 0; female


title: p53NULL_T_rep2

city: Wuerzburg

first: Martin

last: Eilers

address: Am Hubland

department: Chair for Biochemistry and Molecular Biology

institute: University of Wuerzburg

data_processing:
Fastq files were generated using Illumina's CASAVA software and overall sequencing quality was analyzed with the FastQC script.
For mRNA-seq, reads were mapped to hg19 with Tophat2 and Bowtie with default settings.
Reads per gene were counted using the summarizeOverlaps function from the R package {GenomicRanges}, counts per million mapped reads were calculated and log2-transformed.
Genome_build: hg19
Supplementary_files_format_and_content: Sequencing depth normlized count matrix containing Ensembl gene ID and log2-transformed counts per million mapped reads (log2CPM) for all samples and each gene.

source_name: tumors from HCT116_p53NULL cells

growth_protocol: HCT116 p53+/+ and HCT116 p53-/- cells were obtained from B. Vogelstein (Johns Hopkins University, Baltimore) and used at low passage numbers. Cells were cultured in DMEM with 10% foetal bovine serum (FBS, Gibco), 4 mM L-glutamine and 1% penicillin-streptomycin. All cells were cultured at 37°C in a humidified incubator at 5% CO2 and regularly tested to confirm absence of mycoplasma contamination. For spheroid formation, cells were trypsinized, 10000 cells were placed in each well in 96-well ultralow attachment plates (Corning® CORN7007). Spheroid formation was initiated by centrifugation at 850g for 10 min.

extract_protocol:
Total RNA was extracted using Qiagen RNeasy mini columns including on-column DNase I digestion.
mRNA was isolated using the NEBNext® Poly(A) mRNA Magnetic Isolation Module and library preparation was performed with the NEBNext® Ultra™ RNA Library Prep Kit for Illumina following the manufacturer’s instructions. Libraries were size-selected using Agencourt AMPure XP Beads (Beckman Coulter) followed by amplification with 12 PCR cycles. Library quantification and size determination was performed with an Experion automated electrophoresis system (Bio-Rad) and libraries were sequenced with the Illumina NextSeq500.

treatment_protocol: For the simvasttin experiment, HCT116 p53+/+ or p53-/- cells were grown as spheroids and treated with 10 µM simvastatin (SIM) or solvent (DMSO) for 72 hr.

value: tumors from HCT116_p53NULL cells

tag: culture condition

tag: treatment 1

value: constitutive expression of luciferase

tag: treatment 2

value: constitutive shControl

tag: treatment 3

value: Doxycycline in mouse food to induce shRNA expression


title: p53NULL_T_rep3

tag: treatment


title: 151007020_5hmC_Seal

description: Sex: 0; female

tag: age

value: 0; no relapse and death

tag: tissue


title: p53NULL_T_rep1


title: p53WT_T_rep3

source_name: tumors from HCT116_p53WT cells

value: tumors from HCT116_p53WT cells


title: RNAseq2_p53WT_SIM_rep3

tag: cell line

value: spheroid

value: 10µM simvastatin


title: 151107018_5hmC_Seal

description: Sex: 0; female

tag: subject status

value: newly diagnosed patients with DLBCL

tag: race


title: p53WT_T_rep1


title: p53WT_T_rep2


title: RNAseq2_p53WT_SIM_rep1


title: RNAseq2_p53WT_DMSO_rep2

value: DMSO


title: RNAseq2_p53WT_DMSO_rep3


title: RNAseq2_p53NULL_SIM_rep3


title: RNAseq2_p53WT_DMSO_rep1


title: RNAseq2_p53NULL_SIM_rep2


title: 151006036_5hmC_Seal

description: Sex: 0; female

tag: Sex

tag: dlbcl tumor stage

value: GCB


title: RNAseq2_p53NULL_DMSO_rep3


title: 151006035_5hmC_Seal

description: Sex: 1; male

value: male

value: unknown

tag: ldh

tag: deaths=0; alive=1

value: Plasma


title: RNAseq2_p53NULL_DMSO_rep2


title: RNAseq1_p53WT_SPH_rep3


title: RNAseq1_p53NULL_SPH_rep2


title: RNAseq1_p53NULL_SPH_rep3


title: RNAseq1_p53NULL_SPH_rep1


title: RNAseq1_p53WT_SPH_rep1


title: RNAseq1_p53WT_SPH_rep2


title: RNAseq1_p53WT_ML_rep3

value: monolayer


title: RNAseq2_p53WT_SIM_rep2


title: RNAseq1_p53WT_ML_rep2


title: RNAseq1_p53NULL_ML_rep3


title: RNAseq1_p53WT_ML_rep1


title: RNAseq1_p53NULL_ML_rep1


title: RNAseq2_p53NULL_SIM_rep1


title: RNAseq2_p53NULL_DMSO_rep1


title: RNAseq1_p53NULL_ML_rep2


title: Mdc1-/- Abl Pre-B cells, 1 G plus 2 hr, biological rep 3

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: Gene expression 2 hr following exposure to 1 Gy IR of a pMSCV-v-abl retrovirus transformed pre-B cell line from bone marrow harvested from 3 to 5 week old Mdc1-/- mouse that harbored the Em-Bcl2  transgene

hyb_protocol: 15 μg of amplified biotin-cRNAs were fragmented and 10 μg were hybridized to each array for 16 hours at 45°C in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol. Array slides were stained with streptavidin/phycoerythrin utilizing a double-antibody staining procedure and then washed using the EukGE-WS2v5 protocol of the Affymetrix Fluidics Station FS450 for antibody amplification.

scan_protocol: Arrays were scanned in an Affymetrix Scanner 3000.

data_processing: Data was obtained using the GeneChip® Command Console Software (AGCC; Version 1.1) using the MAS5 algorithm to generate .CHP files.

source_name: Abl-transformed Pre-B cells

label_protocol: One μg of total RNA was amplified as directed in the Affymetrix One-Cycle cDNA Synthesis protocol.

growth_protocol: Cells were maintained in suspension in Dulbecco's modified Eagle Medium (DMEM), high glucose, supplemented with 10% fetal bovine serum, 1X Sodium Pyruvate, 1X Non-Essential Amino Acids, 1X L-Glutamine, and 0.0004% b-mercaptoethanol.

extract_protocol: RNA was isolated using a Qiagen RNeasy kit.

treatment_protocol: Cells were exposed to γ-rays from a 137Cesium source at a rate of 0.72 Gy/min for a final dose of 1 Gy.

tag: gene mutated in mouse

value: mediator of DNA damage checkpoint 1 (Mdc1)

value: cultured cell line

value: 2 hr post-exposure to 1 Gy IR


title: 53bp1-/- Abl Pre-B cells, 0 G plus 2 hr, biological rep 2

description: Gene expression from untreated pMSCV-v-abl retrovirus transformed pre-B cell line from bone marrow harvested from 3 to 5 week old 53bp1-/- mouse that harbored the Em-Bcl2 transgene

value: p53-binding protein 1 (53bp1)

value: 2 hr post-exposure to mock treatment (untreated)


title: H2ax-/- Abl Pre-B cells, 1 G plus 2 hr, biological rep 2

description: Gene expression 2 hr following exposure to 1 Gy IR of a pMSCV-v-abl retrovirus transformed pre-B cell line from bone marrow harvested from 3 to 5 week old H2ax-/- mouse that harbored the Em-Bcl2  transgene

value: histone variant H2ax


title: H2ax-/- Abl Pre-B cells, 1 G plus 2 hr, biological rep 1


title: 53bp1-/- Abl Pre-B cells, 1 G plus 2 hr, biological rep 2

description: Gene expression 2 hr following exposure to 1 Gy IR of a pMSCV-v-abl retrovirus transformed pre-B cell line from bone marrow harvested from 3 to 5 week old 53bp1-/- mouse that harbored the Em-Bcl2  transgene


title: Mdc1-/- Abl Pre-B cells, 1 G plus 2 hr, biological rep 2


title: 53bp1-/- Abl Pre-B cells, 1 G plus 2 hr, biological rep 3


title: H2ax-/- Abl Pre-B cells, 0 G plus 2 hr, biological rep 2

description: Gene expression from untreated pMSCV-v-abl retrovirus transformed pre-B cell line from bone marrow harvested from 3 to 5 week old H2ax-/- mouse that harbored the Em-Bcl2 transgene


title: Mdc1-/- Abl Pre-B cells, 0 G plus 2 hr, biological rep 3

description: Gene expression from untreated pMSCV-v-abl retrovirus transformed pre-B cell line from bone marrow harvested from 3 to 5 week old Mdc1-/- mouse that harbored the Em-Bcl2 transgene


title: Mdc1-/- Abl Pre-B cells, 0 G plus 2 hr, biological rep 1


title: 53bp1-/- Abl Pre-B cells, 0 G plus 2 hr, biological rep 3


title: H2ax-/- Abl Pre-B cells, 1 G plus 2 hr, biological rep 3


title: Mdc1-/- Abl Pre-B cells, 0 G plus 2 hr, biological rep 2


title: Mdc1-/- Abl Pre-B cells, 1 G plus 2 hr, biological rep 1


title: H2ax-/- Abl Pre-B cells, 0 G plus 2 hr, biological rep 1


title: Mre11A/A Abl Pre-B cells, 1 G plus 2 hr, biological rep 2

description: Gene expression 2 hr following exposure to 1 Gy IR of a pMSCV-v-abl retrovirus transformed pre-B cell line from bone marrow harvested from 3 to 5 week old Mre11 hypomorph mouse that harbored the Em-Bcl2  transgene

value: Mre11 hypomorph (Mre11A/A)


title: 53bp1-/- Abl Pre-B cells, 1 G plus 2 hr, biological rep 1


title: H2ax-/- Abl Pre-B cells, 0 G plus 2 hr, biological rep 3


title: Mre11A/A Abl Pre-B cells, 1 G plus 2 hr, biological rep 1


title: Mre11A/A Abl Pre-B cells, 1 G plus 2 hr, biological rep 3


title: Mre11A/A Abl Pre-B cells, 0 G plus 2 hr, biological rep 2

description: Gene expression from untreated pMSCV-v-abl retrovirus transformed pre-B cell line from bone marrow harvested from 3 to 5 week old Mre11 hypomorph mouse that harbored the Em-Bcl2 transgene


title: Scid Abl Pre-B cells, 1 G plus 2 hr, biological rep 1

description: Gene expression 2 hr following exposure to 1 Gy IR of a pMSCV-v-abl retrovirus transformed pre-B cell line from bone marrow harvested from 3 to 5 week old Scid mouse that harbored the Em-Bcl2  transgene

value: DNA-PKcs/Prkdc


title: Scid Abl Pre-B cells, 1 G plus 2 hr, biological rep 2


title: Scid Abl Pre-B cells, 0 G plus 2 hr, biological rep 2

description: Gene expression from untreated pMSCV-v-abl retrovirus transformed pre-B cell line from bone marrow harvested from 3 to 5 week old Scid mouse that harbored the Em-Bcl2 transgene


title: Mre11A/A Abl Pre-B cells, 0 G plus 2 hr, biological rep 1


title: Mre11A/A Abl Pre-B cells, 0 G plus 2 hr, biological rep 3


title: 53bp1-/- Abl Pre-B cells, 0 G plus 2 hr, biological rep 1


title: Scid Abl Pre-B cells, 1 G plus 2 hr, biological rep 3


title: Atm-/- Abl Pre-B cells, 0 G plus 2 hr, biological rep 1

description: Gene expression from untreated pMSCV-v-abl retrovirus transformed pre-B cell line from bone marrow harvested from 3 to 5 week old Atm-/- mouse that harbored the Em-Bcl2 transgene

value: Ataxia telangiectasia mutated (Atm)


title: Atm-/- Abl Pre-B cells, 1 G plus 2 hr, biological rep 2

description: Gene expression 2 hr following exposure to 1 Gy IR of a pMSCV-v-abl retrovirus transformed pre-B cell line from bone marrow harvested from 3 to 5 week old Atm-/- mouse that harbored the Em-Bcl2  transgene


title: Atm-/- Abl Pre-B cells, 1 G plus 2 hr, biological rep 1


title: WT Abl Pre-B cells, 1 G plus 2 hr, biological rep 4

description: Gene expression 2 hr following exposure to 1 Gy IR of a pMSCV-v-abl retrovirus transformed pre-B cell line from bone marrow harvested from 3 to 5 week old mouse that harbored the Em-Bcl2 transgene


title: WT Abl Pre-B cells, 0 G plus 2 hr, biological rep 3

description: Gene expression from untreated pMSCV-v-abl retrovirus transformed pre-B cell line from bone marrow harvested from 3 to 5 week old mouse that harbored the Em-Bcl2 transgene


title: Scid Abl Pre-B cells, 0 G plus 2 hr, biological rep 1


title: WT Abl Pre-B cells, 0 G plus 2 hr, biological rep 1


title: WT Abl Pre-B cells, 0 G plus 2 hr, biological rep 4


title: I3a, technical rep1

city: Baltimore

first: Sascha

last: du Lac

state: MD

address: 720 Rutland Avenue

department: Otolaryngology HNS

institute: Johns Hopkins University School of Medicine

hyb_protocol: Hybridization and scanning were done at Salk Institute Functional Genomics Core (La Jolla CA) according to manufacture’s instruction.

data_processing: The data were analyzed with Bioconductor (bioconductor.org) using package affy and gcrma. Default analysis setting of the packages were used. Probe sets designed for outside of 700 bp from the 3’-end of cDNA were excluded from the analysis. Also probe sets of poor performance were excluded (masker.nci.nih.gov).

source_name: mouse MVN cell type I3a

label_protocol: cDNAs prepared from individual cells were amplified, analyzed and classified as described in Kodama et al., 2012 J Neurosci. cDNAs pooled for each cell type were processed to synthesize labeled cRNA as described in Kurimoto et al., 2007 Nat Protocols.

value: brainstem

tag: genotype

value: YFP-16, GIN, and GlyT2-13 lines

tag: background strain


title: I3a, technical rep2

scan_protocol: Hybridization and scanning were done at Salk Institute Functional Genomics Core (La Jolla CA) according to manufacture’s instruction.

extract_protocol: cDNAs prepared from individual cells were amplified, analyzed and classified as described in Kodama et al., 2012 J Neurosci. cDNAs pooled for each cell type were processed to synthesize labeled cRNA as described in Kurimoto et al., 2007 Nat Protocols.


title: E2, technical rep1

source_name: mouse MVN cell type E2


title: I3b, technical rep1

source_name: mouse MVN cell type I3b


title: Atm-/- Abl Pre-B cells, 0 G plus 2 hr, biological rep 2


title: Atm-/- Abl Pre-B cells, 0 G plus 2 hr, biological rep 3


title: E1, technical rep1

source_name: mouse MVN cell type E1


title: I3b, technical rep2


title: I1a, technical rep1

source_name: mouse MVN cell type I1a


title: I1a, technical rep2


title: I2, technical rep1

source_name: mouse MVN cell type I2


title: I1b, technical rep2

source_name: mouse MVN cell type I1b


title: E2, technical rep2


title: Healthy donor #3 C-DC

city: Buffalo

first: Jason

last: Muhitch

state: NY

address: Elm & Carlton Sts.

department: Urology

institute: Roswell Park Cancer Institute

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing: The data were quantile normalized in R

source_name: classical monocyte derived dendritic cell

label_protocol: standard Illumina protocol

extract_protocol: RNA was extracted with Trizol reagent.

tag: monocyte subset

value: classical

tag: cell type

value: dendritic cells


title: WT Abl Pre-B cells, 1 G plus 2 hr, biological rep 1


title: E1, technical rep2


title: I2, technical rep2


title: WT Abl Pre-B cells, 1 G plus 2 hr, biological rep 3


title: Scid Abl Pre-B cells, 0 G plus 2 hr, biological rep 3


title: Healthy donor #3 NC-DC

source_name: non-classical monocyte derived dendritic cell

value: non-classical


title: Healthy donor #2 C-DC


title: Healthy donor #1 C-DC


title: Healthy donor #2 NC-DC


title: Healthy donor #3 C-Mo

source_name: classical monocytes

value: nonocytes


title: Healthy donor #1 NC-DC


title: Healthy donor #3 NC-Mo

source_name: non-classical monocytes


title: Healthy donor #2 C-Mo


title: control 8 C-Mo

extract_protocol: RNA was extracted using Trizol reagent.

tag: disease state

value: control


title: patient 4 follow up draw C-Mo

value: renal cell carcinoma (RCC)


title: control 10 C-Mo


title: control 11 C-Mo


title: I1b, technical rep1


title: Healthy donor #1 NC-Mo


title: patient 17 follow up draw C-Mo


title: patient 17 C-Mo


title: Healthy donor #1 C-Mo


title: patient 5 follow up draw C-Mo


title: patient 4 C-Mo


title: patient 11 C-Mo


title: patient 10 C-Mo


title: patient #2 NC-Mo

value: renal cell carcinoma


title: patient 5 C-Mo


title: patient #11 NC-Mo


title: patient 2 C-Mo


title: patient #17 NC-Mo


title: patient #4 NC-Mo


title: patient #11 I-Mo

source_name: intermediate monocytes

value: intermediate


title: patient #1 NC-Mo


title: patient #5 NC-Mo


title: 11_5PiR2

city: Pozuelo de Alracon

first: Juan

middle: Carlos

last: del Pozo

state: Madrid

address: Campus de Montegancedo, UPM

department: Biotechnology

institute: Centro de Biotecnología y Genómica de Plantas

description: grown without phosphate

data_processing:
Basecalls performed using CASAVA version 1.4
Clean (FastQC software (Babraham-Bioinformatics, 2014).  Reads are mapped to a reference sequences using HISAT2 with 8 mismatches allowed.
Reads count to a reference  genome  (TAIR 42.gff3) using the htseq-count tool.
Differential expression analysis was calculated with edgeR with the following parameters: FDR<0.05, fold change >2 fold  or   < -2 fold
Genome_build: Arabidopsis thaliannTAIR 10
Supplementary_files_format_and_content: tab-delimited text files including normalized counts.

organism: Arabidopsis thaliana

source_name: roots

growth_protocol: Arabidopsis thalinaan (Col-0) seedlings were grown  in Murashige and Skoog medium containing 625 or 5 µM of phosphate for 8 days

extract_protocol:
Total  RNA was isolated from Arabidopsis plants using the Trizol reagent and RNeasy columns (Qiagen). Quantity and quality measurements were taken using a NanoDrop spectrophotometer and Bioanalyzer.
After the total RNA extraction and DNase I treatment, magnetic beads with Oligo (dT) are used to isolate mRNA. Mixed with the fragmentation buffer, the mRNA is fragmented into short fragments. Then cDNA is synthesized using the mRNA fragments as templates. Short fragments are purified and resolved with EB buffer for end reparation and single nucleotide A (adenine) addition. After that, the short fragments are connected with adapters. After agarose gel electrophoresis, the suitable fragments are selected for the PCR amplification as templates. During the QC steps, Agilent  2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System are used in quantification and qualification of the sample library. At last, the library could be sequenced using  Illumina HiSeqTM 2000 or other sequencer when necessary

tag: ecotype

value: Columbia


title: patient #4 I-Mo


title: patient #2 I-Mo


title: 7_5Pi_R1

description: grown without phosphate


title: patient #13 NC-Mo


title: control #10 NC-Mo


title: patient #13 I-Mo


title: control #8 NC-Mo


title: control #11 NC-Mo


title: patient #17 I-Mo


title: control #9 I-Mo


title: patient #2 C-Mo


title: patient #10 I-Mo


title: control #8 I-Mo


title: patient #1 I-Mo


title: patient #17 C-Mo


title: 5_+Pi_R2

description: grown with phosphate


title: control #11 I-Mo


title: patient #5 I-Mo


title: 1_+Pi_R1

description: grown with phosphate


title: patient #10 NC-Mo


title: patient #11 C-Mo


title: control #9 NC-Mo


title: patient #4 C-Mo


title: control #10 I-Mo


title: NP-T4-M3

city: Palaiseau

first: Adeline

last: SIMON

address: 22 place de l'agronomie

institute: INRAE

data_processing:
Sequenced reads were mapped to BcinB0510 Botrytis cinerea genome (fungi.ensembl.org/Botrytis_cinerea/) using STAR-2.5.1b with parameters --alignIntronMin 20 --alignIntronMax 5000 --quantMode GeneCounts
Raw count data were submitted to DESeq2 for normalization and differential analysis
Genome_build: BcinB0510 Botrytis cinerea genome (fungi.ensembl.org/Botrytis_cinerea/)
Supplementary_files_format_and_content: Matrix tables (tab-delimited text files) with either raw values or normalized values for all features.

organism: Botrytis cinerea

source_name: Botrytis cinerea B0510_NonPathogenic-T4

growth_protocol: Wild type B05.10 and  4 non-pathogenic mutants were grown for 48 h at 21°C in liquid cucumber medium at 100 rpm.

extract_protocol:
RNA was extracted using RNeasy plant midi kit (Qiagen). Traces of genomic DNA were removed by DNase treatment.
cDNA single-end libraries were prepared and sequenced (50 pb) on a HiSeq2500 Illumi-na platform at ViroScan-ProfileXpert (France)

tag: strain

value: Mutant NonPathogenic-T4


title: NP-T3-M4

source_name: Botrytis cinerea B0510_NonPathogenic-T3

value: Mutant NonPathogenic-T3


title: NP-T4-M4


title: NP-T2-M4

source_name: Botrytis cinerea B0510_NonPathogenic-T2

value: Mutant NonPathogenic-T2


title: NP-T3-M3


title: High glutamine incubation (10 mM) in human in vitro differentiated adipocyte_input [ChIP-seq]

data_processing:
Sequence data were generated with Illumina HiSeq 2000 single-read sequencing and aligned against the human genome (hg38, GRCh38) using Burrows-Wheeler Aligner (Li and Durbin, 2009) with default parameters.
For O-GlcNAc, peak calling was performed with HOMER (v4.8, 1-13-2016, http://homer.salk.edu.homer/ ) to determine enrichment over the input samples across the whole genome.
Peak size was optimized to 1000 bp, with the minimum distance to the next peak set to 2500 bp.
Genome_build: Human genome (hg38, GRCh38)
Supplementary_files_format_and_content: bedGraph files

source_name: human in vitro differentiated adipocyte day 11 treated with 10 mM of glutamine during differentiation

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIP-seq libraries were prepared using NEBNext ChIP-seq library Prep master mix set (New England Biolabs, USA).

treatment_protocol: Human in vitro differentiated adipocyte day 11 treated with 0.5 mM (L) or 10 mM (H) of glutamine during differentiation.

value: in vitro differentiated adipocyte

tag: passages

tag: treatment

value: High glutamine

tag: chip antibody


title: NP-T3-M2


title: control #8 C-Mo

value: healthy


title: High glutamine incubation (10 mM) in human in vitro differentiated adipocyte_IgG [ChIP-seq]

value: IgG


title: control #11 C-Mo


title: patient #10 C-Mo


title: NP-T4-M2


title: control #10 C-Mo


title: control #9 C-Mo


title: Low glutamine incubation (0.5 mM) in human in vitro differentiated adipocyte_input [ChIP-seq]

source_name: human in vitro differentiated adipocyte day 11 treated with 0.5 mM of glutamine during differentiation

value: Low glutamine


title: High glutamine incubation (10 mM) in human in vitro differentiated adipocyte_rep 1 [ChIP-seq]

description: ChIP-OglcNAc_High_Glutamine _1

value: O-Linked N-Acetylglucosamine (RL2) (a2739)


title: High glutamine incubation (10 mM) in human in vitro differentiated adipocyte_rep 2 [ChIP-seq]

description: ChIP-OglcNAc_High_Glutamine _2


title: NP-T2-M1


title: NP-T2-M3


title: Low glutamine incubation (0.5 mM) in human in vitro differentiated adipocyte_IgG [ChIP-seq]


title: Low glutamine incubation (0.5 mM) in human in vitro differentiated adipocyte_rep 2 [ChIP-seq]

description: ChIP-OglcNAc_Low_Glutamine _2


title: NP-T3-M1


title: High glutamine incubation (10 mM) in human in vitro differentiated adipocyte_rep 3 [ChIP-seq]

description: ChIP-OglcNAc_High_Glutamine _3


title: NP-T1-M2

source_name: Botrytis cinerea B0510_NonPathogenic-T1

value: Mutant NonPathogenic-T1


title: WT-M4

source_name: Botrytis cinerea B0510_wild-type


title: NP-T2-M2


title: Low glutamine incubation (0.5 mM) in human in vitro differentiated adipocyte_rep 1 [ChIP-seq]

description: ChIP-OglcNAc_Low_Glutamine _1


title: NP-T1-M3


title: Atm-/- Abl Pre-B cells, 1 G plus 2 hr, biological rep 3

source_name: Abl-transformed Pre-B cells

value: Ataxia telangiectasia mutated (Atm)

tag: tissue

value: cultured cell line

value: 2 hr post-exposure to 1 Gy IR


title: NP-T1-M4


title: Low glutamine incubation (0.5 mM) in human in vitro differentiated adipocyte_rep 3 [ChIP-seq]

description: ChIP-OglcNAc_Low_Glutamine _3


title: NP-T1-M1


title: WT-M3


title: Non_Regen_14 DPA_scRNA-seq

source_name: Adult non-regenerative mesenchymal cap

value: Adult non-regenerative mesenchymal cap

tag: regeneration time point

value: 14 Days

tag: number of digits

tag: age

value: 10 - 12 Weeks

tag: time spent in enzymatic digestion


title: Dmp1CreERT2TdT_Uninjured_scRNA-seq

description: Mice were injected intraperitoneally with 3mg/day of tamoxifen for four consecutive days and uninjured digit tips were harvested after an additional 10 days. When processing the sequencing data, the reads were aligned to the mm10_TdTomato genome.

source_name: Adult distal digit tip

value: Adult distal digit tip

value: 0 Days


title: control sample 3

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

data_processing:
Illumina base calling
BWA mapping
STAR mapping
HTSEQ counting
Genome_build: dm3
Supplementary_files_format_and_content: raw read count

organism: Drosophila melanogaster

source_name: control_skeletal muscle

growth_protocol: none, acquired by dissection

extract_protocol:
RNeasy Micro Kit (Qiagen).
total stranded

treatment_protocol: RNAi

tag: strain background

tag: genotype/variation

value: control

value: skeletal muscle


title: P3_scRNA-seq

source_name: Postnatal distal digit tip

value: Postnatal distal digit tip

value: Post-natal Day 3


title: WT-M2


title: control sample 1


title: E11_scRNA-seq

source_name: Embryonic hindlimb

value: Embryonic hindlimb

value: 6 Embryos; 12 Limbs

value: Embryonic Day 11


title: WT-M1


title: control sample 2


title: dppOE sample 3

source_name: dppOE_skeletal muscle

value: dpp overexpression


title: Non_Regen_10 DPA_scRNA-seq

value: 10 Days


title: Uninjured_scRNA-seq


title: Regen_28 DPA_scRNA-seq

source_name: Adult regenerated digit tip

value: Adult regenerated digit tip

value: 28 Days


title: dppOE sample 2


title: Regen_14_2 DPA_scRNA-seq

source_name: Adult regenerating digit tip

value: Adult regenerating digit tip


title: Regen_14 DPA_scRNA-seq


title: Regen_10 DPA_scRNA-seq


title: dppOE sample 1


title: control RNAi sample 3

source_name: control RNAi_skeletal muscle

value: control RNAi


title: control RNAi sample 1


title: control RNAi sample 2


title: VYS_DFxC_-+_3

city: Munich

first: Daniel

last: Andergassen

address: Biedersteiner Straße 29

institute: Technical University Munich

data_processing:
RNA sequencing data was aligned to the mm10 genome using STAR (version 2.5.0c). Reads mapping to multiple locations were excluded using specific parameters (STAR:--outFilterMultimapNmax 1). Additional parameters for the STAR alignment were a maximum intron size of 100,000 bp and out-filtering of non-canonical splice junctions.
Genome_build: mm10
Supplementary_files_format_and_content: bigbed

molecule: polyA RNA

source_name: extraembryonic placenta

extract_protocol:
RNA was extracted from TRIzol using standard protocols.
The Illumina TruSeq kit was used to create polyA+ libraries from total RNA. We generated strand-specific libraries for tissues collected form the F1 crosses (TruSeq stranded Illumina) and non-strand-specific TruSeq libraries for the adult organs. All the libraries were run on a Bioanalyzer to assess purity, fragment size, and concentration and sequenced on a HiSeq 2500 at Harvard University’s Bauer Sequencing Core (75 bp paired end).

value: extraembryonic placenta

tag: brackground

tag: genotype

tag: Sex

value: F


title: dpp RNAi #2 sample 3

source_name: dpp RNAi #2_skeletal muscle

value: dpp RNAi construct #2


title: dpp RNAi #2 sample 2


title: patient #13 C-Mo

source_name: classical monocytes

value: renal cell carcinoma

tag: monocyte subset

value: classical


title: Regen_7 DPA _scRNA-seq

value: 7 Days

value: 10 - 12 Weeks


title: dpp RNAi #2 sample 1

value: skeletal muscle


title: VYS_DFxC_++_3


title: VYS_DFxC_-+_2


title: VYS_DFxC_++_1


title: dpp RNAi #1 sample 3

source_name: dpp RNAi #1_skeletal muscle

value: dpp RNAi construct #1


title: dpp RNAi #1 sample 2


title: VYS_DFxC_++_2


title: VYS_CxDF_+-_3


title: dpp RNAi #1 sample 1


title: VYS_CxDF_++_3


title: S8: MCF10A-PHF8 shRNA_2 rep2

city: Iowa City

first: Hank

last: Qi

state: IA

address: 1-632 Bowen Science Building

institute: University of Iowa

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then pseudo-aligned using the kallisto method
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited tsv files including lengths, counts and transcripts per million (TPM) for mRNA transcripts

growth_protocol: MCF10A cells were cultured in DMEM-F12 supplemented with 20 ng/ml Epidermal Growth Factor (EGF) (Sigma), 100 ng/ml cholera toxin (Sigma), 10 μg/ml insulin (Sigma), 500 ng/ml hydrocortisone (Sigma), and 5% horse serum. Cells were maintained in the specified medium supplemented with 1× Penicillin–Streptomycin (Gibco) and incubated in 5% CO2 at 37 °C.

extract_protocol:
Total RNA was isolated from MCF10A/control cells using the RNeasy Plus Mini Kit (Qiagen) following the manufacturer’s protocol. RNA-seq libraries were made using the TruSeq Stranded Total RNA LT Sample Prep Kit (with Ribo-Zero™ Human/Mouse/Rat, RS-122-2201) and multiplexed with Illumina barcodes. Two biological duplicates of MCF10A/control samples, HER2 overexpression and two constructs of shRNA PHF8 were sequenced on the HiSeq2500 instrument following protocols supplied by Illumina (San Diego, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols. 50-bp paired-end reads were generated. More than 20 Mb reads were produced for each library.

tag: origin

value: Mammary Epithelial Cells

tag: cell line

tag: cell type

value: breast cancer


title: S7: MCF10A-PHF8 shRNA rep2


title: VYS_CxDF_+-_2

tag: strain


title: VYS_CxDF_++_2


title: S6: MCF10A HER2 rep2


title: S4: MCF10A-PHF8 shRNA_2 rep1


title: S5: MCF10A-scramble shRNA rep2


title: VYS_CxDF_++_1


title: Healthy donor #2 NC-Mo

source_name: non-classical monocytes

value: non-classical

value: nonocytes


title: S3: MCF10A-PHF8 shRNA_1 rep1


title: Pl_DFxC_-+_4


title: VYS_DFxC_-+_1


title: VYS_CxDF_+-_1


title: Pl_CxDF_+-_4


title: S2: MCF10A HER2 rep1